U.S. patent application number 15/030019 was filed with the patent office on 2016-09-08 for allele specific pcr assay for detection of nucleotide variants.
This patent application is currently assigned to University of Pittsburgh - Of the Commonwealth System of Higher Education. The applicant listed for this patent is Elias HALVAS, John MELLORS, Constantinos PANOUSIS, University of Pittsburgh - Of the Commonwealth System of Higher Education. Invention is credited to Elias Halvas, John Mellors, Constantinos Panousis.
Application Number | 20160258010 15/030019 |
Document ID | / |
Family ID | 52828794 |
Filed Date | 2016-09-08 |
United States Patent
Application |
20160258010 |
Kind Code |
A1 |
Panousis; Constantinos ; et
al. |
September 8, 2016 |
ALLELE SPECIFIC PCR ASSAY FOR DETECTION OF NUCLEOTIDE VARIANTS
Abstract
Described herein are improved methods for detecting one or more
alleles of a target nucleic acid molecule in a biological sample.
The methods can be used, for example, for detecting low-frequency
drug resistance mutations of a target nucleic acid molecule in a
biological sample from a subject receiving the drug. In several
embodiments, the subject is a subject with an HIV-1 infection, and
the method is a method of detecting one or more drug-resistance
mutations in an HIV-1 reverse transcriptase gene. Oligonucleotide
primers for use in the disclosed methods, and compositions
comprising same, are also provided.
Inventors: |
Panousis; Constantinos;
(Pittsburgh, PA) ; Halvas; Elias; (Pittsburgh,
PA) ; Mellors; John; (Pittsburgh, PA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
PANOUSIS; Constantinos
HALVAS; Elias
MELLORS; John
University of Pittsburgh - Of the Commonwealth System of Higher
Education |
Pittsburgh
Pittsburgh
Pittsburgh
Pittsburgh |
PA
PA
PA
PA |
US
US
US
US |
|
|
Assignee: |
University of Pittsburgh - Of the
Commonwealth System of Higher Education
Pittsburgh
PA
|
Family ID: |
52828794 |
Appl. No.: |
15/030019 |
Filed: |
October 20, 2014 |
PCT Filed: |
October 20, 2014 |
PCT NO: |
PCT/US14/61377 |
371 Date: |
April 15, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61892993 |
Oct 18, 2013 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2525/186 20130101;
C12Q 1/6858 20130101; C12Q 1/6851 20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Goverment Interests
ACKNOWLEDGMENT OF GOVERNMENT SUPPORT
[0002] This invention was made with government support under Grant
No. AI068633 awarded by the National Institutes of Health. The
government has certain rights in the invention.
Claims
1. A method of detecting a mutant first allele of a target nucleic
acid molecule in a biological sample, comprising: (A) amplifying
the target nucleic acid molecule from the biological sample by
real-time polymerase chain reaction (qPCR) using a test primer pair
in a test amplification, comprising a first plus primer comprising
a locked nucleic acid at the 3' end that is complementary to the
mutant first allele of the target nucleic acid molecule, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule; and a reverse primer of the test primer pair; (B)
amplifying the target nucleic acid molecule from the biological
sample by qPCR using a control set of primers in a control
amplification, comprising the first primer pair; and a first
control primer comprising a locked nucleic acid at the 3' end that
is complementary to a wildtype first allele corresponding to the
mutant first allele, and remaining nucleotides that are the same as
the first plus primer; (C) determining a threshold cycle (Ct) value
of the test amplification and a Ct value of the control
amplification; and (D) comparing a difference between the Ct values
of the test and control amplifications with a standard control
generated using a mixture of target nucleic acid molecules
comprising a pre-selected proportion of the mutant and wildtype
first alleles to detect the mutant first allele of the target
nucleic acid molecule in the biological sample.
2. The method of claim 1, further comprising detecting a mutant
second allele of the target nucleic acid molecule in the biological
sample, wherein: the reverse primer of the test primer pair is a
second plus primer comprising a locked nucleic acid at the 3' end
that is complementary to the mutant second allele, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule; the control set of primers further comprises a second
control primer comprising a locked nucleic acid at the 3' end that
is complementary to a wildtype second allele corresponding to the
mutant second allele, and remaining nucleotides that are the same
as the second plus primer; and the difference between the Ct values
of the test and control amplifications are compared with a standard
control generated using a mixture of target nucleic acid molecules
comprising a pre-selected proportion of the mutant and wildtype
first alleles and the mutant and wildtype second alleles to detect
the mutant first and second alleles of the target nucleic acid
molecule in the biological sample.
3. The method of claim 1, wherein the control set of primers
further comprises: a third control primer, comprising a locked
nucleic acid at the 3' end that is not complementary to the mutant
or wildtype first allele, and remaining nucleotides that are the
same as the first plus primer; and a fourth control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype first allele and is not the
same as the locked nucleic acid of the third control primer, and
remaining nucleotides that are the same as the first plus
primer.
4. The method of claim 2, wherein the control set of primers
further comprises: (a) a third control primer, comprising a locked
nucleic acid at the 3' end that is not complementary to the mutant
or wildtype first allele, and remaining nucleotides that are the
same as the first plus primer; (b) a fourth control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype first allele and is not the
same as the locked nucleic acid of the third control primer, and
remaining nucleotides that are the same as the first plus primer;
(c) a fifth control primer, comprising a locked nucleic acid at the
3' end that is not complementary to the mutant or wildtype second
allele, and remaining nucleotides that are the same as the second
plus primer; (d) a sixth control primer, comprising a locked
nucleic acid at the 3' end that is not complementary to the mutant
or wildtype second allele and is not the same as the locked nucleic
acid of the fifth control primer, and remaining nucleotides that
are the same as the second plus primer; a combination of (a) and
(b); a combination of (c) and (d); or a combination of (a), (b),
(c), or (d).
5. The method of claim 1, wherein detecting the mutant first allele
of the target nucleic acid molecule in the biological sample
comprises detecting a proportion of the target nucleic acid
molecules in the sample comprising the mutant first allele in the
biological sample, and wherein no more than 20% of the target
nucleic acid molecules in the biological sample comprise the mutant
first allele.
6. The method of claim 5, wherein no more than 1% of the target
nucleic acid molecules in the biological sample comprise the mutant
first allele.
7. The method of claim 1, comprising a first round amplification of
template DNA from the biological sample prior to the test or
control amplifications, wherein the first round amplification
comprises use of a proof-reading DNA polymerase.
8. The method of claim 1, wherein the mutant first allele, the
mutant second allele, or both, is a drug resistant mutant allele of
Human Immunodeficiency Virus (HIV)-1 or HIV-2.
9. The method of claim 8, wherein the mutant first allele, the
mutant second allele, or both, is a drug resistant mutant allele of
HIV-1 reverse transcriptase.
10. The method of claim 9, wherein the mutant first allele encodes
one of the following mutations of HIV-1 reverse transcriptase:
K65R, M184V, M184I, M41L, A62V, K65N, K65E, D67N, D67G, D67E, T69I,
T69D, K70R, K70E, K70G, K70T, K70N, K70Q, L74V, L74I, V75I, V75M,
V75T, F77L, L100I, K101P, K103N, K103S, V106M, Y115F, F116Y, Q151M,
Y181C, Y181I, Y188L, G190S, G190A, L210W, T215Y, T215F, T215E,
T215I, T215C, T215D, K219Q, K219E, K219N, K219R, P225H, or
M230L.
11. The method of claim 9, wherein the first plus primer, the first
control primer, and the reverse primer, comprise or consist of the
nucleic acid sequences set forth as one of: (a) SEQ ID NOs: 1, 2,
and 3, respectively, for detecting a K65R allele; (b) SEQ ID NOs:
29, 41, and 3, respectively, for detecting a K65R allele; (c) SEQ
ID NOs: 40, 42, and 3, respectively, for detecting a K65R allele;
(d) SEQ ID NOs: 1, 2, and 37, respectively, for detecting a K65R
allele; (e) SEQ ID NOs: 29, 41, and 37, respectively, for detecting
a K65R allele; (f) SEQ ID NOs: 40, 42, and 37, respectively, for
detecting a K65R allele; (g) SEQ ID NOs: 1, 2, and 38,
respectively, for detecting a K65R allele; (h) SEQ ID NOs: 29, 41,
and 38, respectively, for detecting a K65R allele; (i) SEQ ID NOs:
40, 42, and 38, respectively, for detecting a K65R allele; (j) SEQ
ID NOs: 4, 5 and 3, respectively, for detecting a K70E allele; (k)
SEQ ID NOs: 4, 5, and 37, respectively, for detecting a K70E
allele; (l) SEQ ID NOs: 4, 5, and 38, respectively, for detecting a
K70E allele; (m) SEQ ID NOs: 6, 7, and 8, respectively, for
detecting a M184V allele; (n) SEQ ID NOs: 9, 10, and 10,
respectively, for detecting a M184I allele; (o) SEQ ID NOs: 11, 12,
and 14, respectively, for detecting a K103N allele; (p) SEQ ID NOs:
15, 12, and 14, respectively, for detecting a K103N allele; (q) SEQ
ID NOs: 16, 17, and 17, respectively, for detecting a Y181C allele;
or (r) SEQ ID NOs: 19, 20, and 20, respectively, for detecting a
G190A allele.
12. The method of claim 9, wherein the first and second alleles are
selected from one of: K65R and M184V, respectively; K65R and M184I,
respectively; K65R and K103N, respectively; K70E and M184V,
respectively; K70E and M184I, respectively; K70E and K103N,
respectively; K103N and M184V, respectively; or K103N and M184I,
respectively.
13. The method of claim 2, wherein (a) the first and second mutant
alleles are K65R and M184V mutant alleles of HIV-1 reverse
transcriptase, respectively, and wherein the first plus primer, the
first control primer, the second plus primer, and the second
control primer, comprise or consist of the nucleic acid sequences
set forth as SEQ ID NOs: 1, 2, 6, and 7, respectively; or (b) the
first and second mutant alleles are K65R and M184I mutant alleles
of HIV-1 reverse transcriptase, respectively, and wherein the first
plus primer, the first control primer, the second plus primer, and
the second control primer, comprise or consist of the nucleic acid
sequences set forth as SEQ ID NOs: 1, 2, 9, and 10,
respectively.
14. The method of claim 1, wherein the subject has an HIV-1
infection.
15. The method of claim 14, wherein the subject is being treated
with a combination of tenofovir and emtricitabine.
16. The method of claim 8, further comprising identifying the
subject as having a drug-resistant mutant allele of HIV-1 or
HIV-2.
17. An isolated nucleic acid molecule, comprising a plus primer
comprising or consisting of the nucleic acid sequence set forth as
any one of SEQ ID NOs: 1-2, 4-5, 6-7, 9-12, 15-17, 19-20, or
39-42.
18. A composition, comprising: (A) a primer pair comprising a
forward and a reverse primer for amplifying a target nucleic acid
molecule comprising a mutant first allele of a target nucleic acid;
wherein the forward primer is a first plus primer comprising a
locked nucleic acid at the 3' end that is complementary to the
mutant first allele of the target nucleic acid molecule, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule; and (B) a first control primer comprising a locked
nucleic acid at the 3' end that is complementary to a wildtype
first allele corresponding to the mutant first allele, and
remaining nucleotides that are the same as the first plus
primer.
19. The composition of claim 18, wherein the first plus primer, the
first control primer, and the reverse primer, comprise or consist
of the nucleic acid sequences set forth as: (a) SEQ ID NOs: 1, 2,
and 3, respectively; (b) SEQ ID NOs: 29, 41, and 3, respectively;
(c) SEQ ID NOs: 40, 42, and 3, respectively; (d) SEQ ID NOs: 1, 2,
and 37, respectively; (e) SEQ ID NOs: 29, 41, and 37, respectively;
(f) SEQ ID NOs: 40, 42, and 37, respectively; (g) SEQ ID NOs: 1, 2,
and 38, respectively; (h) SEQ ID NOs: 29, 41, and 38, respectively;
(i) SEQ ID NOs: 40, 42, and 38, respectively; (j) SEQ ID NOs: 4, 5
and 3, respectively; (k) SEQ ID NOs: 4, 5, and 37, respectively;
(l) SEQ ID NOs: 4, 5, and 38, respectively; (m) SEQ ID NOs: 6, 7,
and 8, respectively; (n) SEQ ID NOs: 9, 10, and 10, respectively;
(o) SEQ ID NOs: 11, 12, and 14, respectively; (p) SEQ ID NOs: 15,
12, and 14, respectively; (q) SEQ ID NOs: 16, 17, and 17,
respectively; or (r) SEQ ID NOs: 19, 20, and 20, respectively.
20. The composition of claim 18, wherein the target nucleic acid
molecule further comprises a second allele, and wherein the reverse
primer of the test primer pair is a second plus primer comprising a
locked nucleic acid at the 3' end that is complementary to the
mutant second allele, a mismatch nucleotide at the -1 position from
the 3' end that is not complementary to the target nucleic acid
molecule, and remaining nucleotides that are complementary to the
target nucleic acid molecule; and the composition further comprises
a second control primer comprising a locked nucleic acid at the 3'
end that is complementary to a wildtype second allele corresponding
to the mutant second allele, and remaining nucleotides that are the
same as the second plus primer.
21. The composition of claim 20, wherein the first plus primer, the
first control primer, the second plus primer, and the second
control primer, comprise or consist of the nucleic acid sequences
set forth as SEQ ID NOs: 1, 2, 6, and 7, respectively; or SEQ ID
NOs: 1, 2, 9, and 10, respectively.
22. The composition of claim 18, further comprising: a third
control primer, comprising a locked nucleic acid at the 3' end that
is not complementary to the mutant or wildtype first allele, and
remaining nucleotides that are the same as the first plus primer;
and the fourth control primer, comprising a locked nucleic acid at
the 3' end that is not complementary to the mutant or wildtype
first allele and is not the same as the locked nucleic acid of the
third control primer, and remaining nucleotides that are the same
as the first plus primer.
23. The composition of claim 22, further comprising (a) a third
control primer, comprising a locked nucleic acid at the 3' end that
is not complementary to the mutant or wildtype first allele, and
remaining nucleotides that are the same as the first plus primer;
(b) a fourth control primer, comprising a locked nucleic acid at
the 3' end that is not complementary to the mutant or wildtype
first allele and is not the same as the locked nucleic acid of the
third control primer, and remaining nucleotides that are the same
as the first plus primer; (c) a fifth control primer, comprising a
locked nucleic acid at the 3' end that is not complementary to the
mutant or wildtype second allele, and remaining nucleotides that
are the same as the second plus primer; (d) a sixth control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype second allele and is not
the same as the locked nucleic acid of the fifth control primer,
and remaining nucleotides that are the same as the second plus
primer; a combination of (a) and (b); a combination of (c) and (d);
or a combination of (a), (b), (c), or (d).
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional
Application No. 61/892,993, filed Oct. 18, 2013, which is
incorporated by reference in its entirety.
FIELD
[0003] This application relates to the field of detecting minor or
major genomic variants in a polymorphic background, particularly to
methods and compositions for identifying drug-resistant viral
strains.
BACKGROUND
[0004] Variations in the nucleotide sequence of DNA impact if and
how an organism develops diseases, and respond to pathogens,
chemicals, drugs, vaccines and other agents.
[0005] Several assays have been developed for detection of the
presence of low-frequency drug-resistant nucleotide mutations in a
clinical sample, including Ultra-Deep Pyrosequencing (UDPS), Single
Genome Sequencing (SGS), and Allele-Specific Polymerase Chain
Reaction (ASPCR). UDPS is characterized by the sequencing of many
genomes in a single run and the detection of low-frequency variants
down to one percent. UDPS is more sensitive than standard
sequencing and can lower the risk of virologic failure, but it is
very expensive and requires extensive sequence alignment
computation. SGS is characterized by the sequencing of 45-50
individual clones and a sensitivity of minor variant detection down
to five percent. However, SGS sensitivity is limited by the number
of clones tested, and the assay suffers from high cost and labor
intensity. ASPCR is a quantitative real-time polymerase chain
reaction (qPCR)-based assay where one of the amplification primers
includes a 3' nucleotide that is complementary to a mutant allele
of interest and not complementary to the wild-type allele.
Detection is achieved by the higher amplification efficiency on
mutant sequence versus the wild type sequence. Although ASPCR
assays are low cost and sensitive, the clinical utility of current
ASPCR assays is limited due to false negative and positive
artifacts caused by DNA polymorphisms that affect primer binding,
as well as the inability to detect more than one polymorphism in a
single assay.
SUMMARY
[0006] Provided herein is a modified ASPCR assay that addresses
many of the issues associated with current methodologies. The
disclosed methods have increased sensitivity, minimize false
positive results and high background, can detect linkage between
two polymorphisms (e.g., drug resistance mutations) in a target
nucleic acid molecule, and are designed to minimize variability
associated with target polynucleotide polymorphism. In some
embodiments, the methods can be used to detect a mutant allele of a
target nucleic acid molecule that is associated with
drug-resistance to a particular therapy, such as antiretroviral
therapy for Human Immunodeficiency Virus (HIV)-1 infection.
[0007] Several embodiments include a method of detecting a mutant
first allele of a target nucleic acid molecule in a biological
sample. The method includes a test amplification and a control
amplification. The test amplification includes amplifying the
target nucleic acid molecule from the biological sample by qPCR
using a test primer pair comprising a first plus primer comprising
a locked nucleic acid at the 3' end that is complementary to the
mutant first allele of the target nucleic acid molecule, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule, and a reverse primer of the test primer pair. The control
amplification includes amplifying the target nucleic acid molecule
from the biological sample by qPCR using a control set of primers
comprising the first primer pair, and a first control primer
comprising a locked nucleic acid at the 3' end that is
complementary to a wildtype first allele corresponding to the
mutant first allele, and remaining nucleotides that are the same as
the first plus primer. The threshold cycle (Ct) value of the test
amplification and the Ct value of the control amplification are
measured. A difference between the Ct value of the test
amplification and the Ct value of the control amplification is
compared with a standard control generated using a mixture of
target nucleic acid molecules comprising a pre-selected proportion
of the mutant and wildtype first alleles to detect the first allele
of the target nucleic acid molecule in the biological sample.
[0008] In several embodiments, detecting the mutant first allele of
the target nucleic acid molecule in the biological sample comprises
detecting a proportion of target nucleic acid molecules in the
biological sample that comprises the first allele. In several
embodiments, no more than 20% (such as no more than 1%) of the
target nucleic acid molecules in the biological sample comprise the
mutant first allele.
[0009] In other embodiments, the method can further include
detecting a mutant second allele of the target nucleic acid
molecule in the biological sample, wherein the reverse primer of
the test primer pair is a second plus primer comprising a locked
nucleic acid at the 3' end that is complementary to the mutant
second allele, a mismatch nucleotide at the -1 position from the 3'
end that is not complementary to the target nucleic acid molecule,
and remaining nucleotides that are complementary to the target
nucleic acid molecule; and the control set of primers further
comprises a second control primer comprising a locked nucleic acid
at the 3' end that is complementary to a wildtype second allele
corresponding to the mutant second allele, and remaining
nucleotides that are the same as the second plus primer. The
difference between the Ct values of the test and control
amplifications are compared with a standard control generated using
a mixture of target nucleic acid molecules comprising a
pre-selected proportion of the mutant and wildtype first alleles
and the mutant and wildtype second alleles to detect the mutant
first and second alleles of the target nucleic acid molecule in the
biological sample.
[0010] In a non-limiting example, the disclosed methods can be used
to identify a K65R and/or M184V mutant allele of HIV-1 reverse
transcriptase in a biological sample, for example, a biological
sample from a subject with HIV-1 infection.
[0011] Reagents (for example, novel oligonucleotide primers and
compositions comprising same) and kits for use in the disclosed
methods are also provided.
[0012] The foregoing and other features and advantages of this
disclosure will become more apparent from the following detailed
description of several embodiments which proceeds with reference to
the accompanying figures.
BRIEF DESCRIPTION OF THE FIGURES
[0013] FIG. 1 is a graph illustrating discrimination between mutant
(65R) and wild type (65K) templates for three ASPCR primer designs
at two annealing temperatures of 55 and 61.degree. C. The primers
used included a locked nucleic acid at the 3' end (LNA), a mismatch
at the penultimate site (PEN), or a combination of the LNA and PEN
(PLUS). Discriminatory power of the assay is expressed as
.DELTA.Ct.
[0014] FIGS. 2A and 2B are a set of graphs illustrating validation
of the disclosed ASPCR assay with M184V and M184I target nucleic
acids. Both Plus and PEN primers for M184V and M184I were of
identical sequence. PLUS primers were additionally modified with a
3' end LNA. ASPCR was performed over a range of annealing
temperatures ranging from 55.degree. C. to 65.degree. C. .DELTA.Ct
corresponds to change in Ct.
[0015] FIGS. 3A-3C are a series of schematic diagrams illustrating
the prior method for detecting total target DNA in an ASPCR assay,
as well as the new method disclosed herein. (A) Old method; Assay
is normalized against a total reaction either at a different or at
the same site as the allele specific reaction. (B) Total primer
missing the 3' mismatch does not translate to same amplification
efficiency, as mismatches present close to 3' can have deleterious
effects on amplification efficiency. (C) New method; Assay is
normalized using the exact same amplicon and 3' degenerative
primers for the mutation in question.
[0016] FIG. 4 shows a set of graphs illustrating the reduction of
background and limit of detection using a proof reading polymerase.
Ten clinical samples were tested by the disclosed ASPCR assay for
K65R and M184V using either a non-proof reading polymerase (Taq) or
a proof-reading polymerase (Phusion).
[0017] FIGS. 5A and 5B are a graph and a schematic representation
illustrating the detection of linked resistance mutations using the
disclosed ASPCR assay. (A) Detection of linked K65R and M184V
mutations by ASPCR utilizing a K65R allele specific forward primer
and a M184V allele specific reverse primer. (B) Illustration of
templates and normalization reaction for standards and samples.
[0018] FIG. 6 is a table showing a comparison between an older
ASPCR method and the disclosed ASPCR assay for detection of mutant
alleles in clinical samples. Percentage shown in parentheses is
estimated based on electropherogram.
[0019] FIG. 7 is a table showing the validation of the disclosed
ASPCR assay for detecting a M184V allele in pre-made viral mixtures
of wild-type and M184 V HIV-1, spiked in human negative plasma.
[0020] FIG. 8 is a table showing the detection of linked K65R/M184V
resistance mutations using the disclosed ASPCR assay.
[0021] FIG. 9 shows a schematic diagram and a set of graphs
illustrating improved methods for normalization of ASPCR
assays.
[0022] FIG. 10 is a set of graphs illustrating that the disclosed
ASPCR assay can successfully detect mutant alleles from HIV-1
sub-types with polymorphic differences.
SEQUENCE LISTING
[0023] The nucleic and amino acid sequences listed in the
accompanying sequence listing are shown using standard letter
abbreviations for nucleotide bases, and three letter code for amino
acids, as defined in 37 C.F.R. 1.822. Only one strand of each
nucleic acid sequence is shown, but the complementary strand is
understood as included by any reference to the displayed strand.
The Sequence Listing is submitted as an ASCII text file in the form
of the file named "Sequence.txt" (.about.20 kb), which was created
on Oct. 17, 2014, which is incorporated by reference herein. In the
accompanying sequence listing:
[0024] SEQ ID NOs: 1, 4, 6, 9, 11, 15-16, 19, and 39-40 are the
nucleic acid sequences of allele-specific Plus primers including a
mismatch nucleotide at the -1 position from the '3 end and a locked
nucleic acid at the 3' end that is complementary to mutant allele
sequence.
[0025] SEQ ID NOs: 2, 5, 7, 10, 12, 17, 20, and 41-42 are the
nucleic acid sequences of wildtype-specific Control primers
including a mismatch nucleotide at the -1 position from the '3 end
and a locked nucleic acid at the 3' end that is complementary to
wildtype sequence.
[0026] SEQ ID NOs: 11, 13, 15, 33-34, and 43-46 are the nucleic
acid sequences of additional control primers including a mismatch
nucleotide at the -1 position from the '3 end and a locked nucleic
acid at the 3' end that is not complementary to wildtype or mutant
allele sequence.
[0027] SEQ ID NOs: 3, 8, 14, 18, 37, and 38 are the nucleic acid
sequences of reverse oligonucleotide primers.
[0028] SEQ ID NOs: 21-31, and 35 are the nucleic acid sequences of
oligonucleotide primers.
[0029] SEQ ID NO: 32 is the nucleotide sequence of genomic DNA
encoding wild-type HIV-1 reverse transcriptase (HXB2 strain).
[0030] SEQ ID NO: 36 is the amino acid sequence of wild-type HIV-1
reverse transcriptase p66 subunit (HXB2 strain).
DETAILED DESCRIPTION
I. Summary of Terms
[0031] Unless otherwise noted, technical terms are used according
to conventional usage. Definitions of common terms in molecular
biology may be found in Benjamin Lewin, Genes X, published by Jones
& Bartlett Publishers, 2009; and Meyers et al. (eds.), The
Encyclopedia of Cell Biology and Molecular Medicine, published by
Wiley-VCH in 16 volumes, 2008; and other similar references.
[0032] As used herein, the singular forms "a," "an," and "the,"
refer to both the singular as well as plural, unless the context
clearly indicates otherwise. As used herein, the term "comprises"
means "includes." It is further to be understood that any and all
base sizes or amino acid sizes, and all molecular weight or
molecular mass values, given for nucleic acids or polypeptides are
approximate, and are provided for descriptive purposes, unless
otherwise indicated. Although many methods and materials similar or
equivalent to those described herein can be used, particular
suitable methods and materials are described below. In case of
conflict, the present specification, including explanations of
terms, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting. To
facilitate review of the various embodiments, the following
explanations of terms are provided:
[0033] 3' end: The end of a nucleic acid molecule that does not
have a nucleotide bound to it 3' of the terminal residue.
[0034] 5' end: The end of a nucleic acid sequence where the 5'
position of the terminal residue is not bound by a nucleotide.
[0035] Allele: A particular form of a genetic locus, distinguished
from other forms by its particular nucleotide sequence, or one of
the alternative polymorphisms found at a polymorphic site.
[0036] Allele-specific: A particular position of a nucleic acid
sequence that, with reference oligonucleotides and primers, is
complementary with an allele of a target polynucleotide sequence.
Allele-specific primers are capable of discriminating between
different alleles of a target polynucleotide. It is understood that
several disclosed oligonucleotides include deliberate mismatches
(at a different position than the allele-specific nucleotide) such
that the oligonucleotide is not exactly complementary to the target
polynucleotide. The function of the allele-specific
oligonucleotides (e.g., plus primers) is to facilitate preferential
hybridization and extension under PCR conditions of primers having
the allele-specific nucleotide, or, alternatively, suppressing
hybridization and extension of primers not having the
allele-specific nucleotide.
[0037] Amplification: A technique that increases the number of
copies of a nucleic acid molecule (such as an RNA or DNA). An
example of amplification is polymerase chain reaction (PCR), in
which a sample is contacted with a pair of oligonucleotide primers
under conditions that allow for the hybridization of the primers to
a nucleic acid template in the sample. The primers are extended
under suitable conditions (e.g., in the presence of a polymerase
enzyme and dNTPs), dissociated from the template, re-annealed,
extended, and dissociated to amplify the number of copies of the
nucleic acid. The product of amplification can be characterized by
electrophoresis, restriction endonuclease cleavage patterns,
oligonucleotide hybridization or ligation, and/or nucleic acid
sequencing using standard techniques.
[0038] Other examples of amplification include quantitative
real-time polymerase chain reaction (qPCR), strand displacement
amplification, as disclosed in U.S. Pat. No. 5,744,311;
transcription-free isothermal amplification, as disclosed in U.S.
Pat. No. 6,033,881; repair chain reaction amplification, as
disclosed in PCT publication WO 90/01069; ligase chain reaction
amplification, as disclosed in European patent publication
EP-A-320,308; gap filling ligase chain reaction amplification, as
disclosed in U.S. Pat. No. 5,427,930; and NASBA RNA
transcription-free amplification, as disclosed in U.S. Pat. No.
6,025,134. Several embodiments include multiplex qPCR assays, which
are useful for amplifying and detecting multiple nucleic acid
sequences in a single reaction.
[0039] Biological sample: A sample of biological material obtained
from a subject. Biological samples include all clinical samples
useful for detection of disease or infection (e.g., HIV infection)
in subjects. Appropriate samples include any conventional
biological samples, including clinical samples obtained from a
human or veterinary subject. Exemplary samples include, without
limitation, cells, cell lysates, blood smears, cytocentrifuge
preparations, cytology smears, bodily fluids (e.g., blood, plasma,
serum, saliva, sputum, urine, bronchoalveolar lavage, semen,
cerebrospinal fluid (CSF), etc.), tissue biopsies or autopsies,
fine-needle aspirates, and/or tissue sections. In a particular
example, a biological sample is obtained from a subject having,
suspected of having or at risk of having HIV infection.
[0040] Complementary. Complementary binding occurs when the base of
one nucleic acid molecule forms a hydrogen bond to the base of
another nucleic acid molecule. Normally, the base adenine (A) is
complementary to thymidine (T) and uracil (U), while cytosine (C)
is complementary to guanine (G). For example, the sequence
5'-ATCG-3' of one ssDNA molecule can bond to 3'-TAGC-5' of another
ssDNA to form a dsDNA. In this example, the sequence 5'-ATCG-3' is
the reverse complement of 3'-TAGC-5'.
[0041] Nucleic acid molecules can be complementary to each other
even without complete hydrogen-bonding of all bases of each
molecule. For example, hybridization with a complementary nucleic
acid sequence can occur under conditions of differing stringency in
which a complement will bind at some but not all nucleotide
positions. In particular examples disclosed herein, the
complementary sequence is complementary at a labeled nucleotide,
and at each nucleotide immediately flanking the labeled
nucleotide.
[0042] Consists of or consists essentially of: With regard to a
polynucleotide (such as a probe or primer), a polynucleotide
consists essentially of a specified nucleotide sequence if it does
not include any additional nucleotides. However, the polynucleotide
can include additional non-nucleic acid components, such as labels
(for example, fluorescent, radioactive, or solid particle labels),
sugars or lipids. With regard to a polynucleotide, a polynucleotide
that consists of a specified nucleotide sequence does not include
any additional nucleotides, nor does it include additional
non-nucleic acid components, such as lipids, sugars or labels.
[0043] Contacting: Placement in direct physical association, for
example solid, liquid or gaseous forms. Contacting includes, for
example, direct physical association of fully- and
partially-solvated molecules.
[0044] Control: A sample or standard used for comparison with an
experimental sample. In some embodiments, the control is a sample
obtained from a healthy patient, or a sample from a subject with
HIV. In some embodiments, the control is a sample including HIV
nucleic acid. In other embodiments, the control is a biological
sample obtained from a patient diagnosed with HIV. In still other
embodiments, the control is a historical control or standard
reference value or range of values (such as a previously tested
control sample, such as a group of HIV patients with known
prognosis or outcome, or group of samples that represent baseline
or normal values, such as the presence or absence of HIV in a
biological sample.
[0045] In some embodiments, the results of an ASPCR assay performed
on a test sample using primer sets as described herein can be
compared with a standard control (such as a standard curve)
generated using an ASPCR assay with the same primer sets that is
performed on a mixture of target nucleic acid molecules comprising
a pre-selected proportion of mutant and wildtype alleles to detect
the presense (or proportion) of a particular allele in the test
sample.
[0046] Ct (threshold cycle): The PCR cycle number at which the
fluorescence emission (dRn) exceeds a chosen threshold, which is
typically 10 times the standard deviation of the baseline (this
threshold level can, however, be changed if desired). The threshold
cycle is when the system begins to detect the increase in the
signal associated with an exponential growth of PCR product during
the log-linear phase. This phase provides information about the
reaction. The slope of the log-linear phase is a reflection of the
amplification efficiency. The efficiency of the reaction can be
calculated by the following equation: E=10.sup.(-1/slope), for
example. The efficiency of the PCR should be 90-100% meaning
doubling of the amplicon at each cycle. This corresponds to a slope
of -3.1 to -3.6 in the C.sub.t vs. log-template amount standard
curve.
[0047] Detecting: To identify the existence, presence, or fact of
something. General methods of detecting are known to the skilled
artisan and may be supplemented with the protocols and reagents
disclosed herein. For example, included herein are methods of
detecting HIV in a biological sample, including detecting a
particular HIV allele in a biological sample, such as a drug
resistant allele. Detection can include a physical readout, such as
fluorescence or a reaction output, or the results of PCR (such as
qPCR) assay.
[0048] Detectable marker: A detectable molecule (also known as a
label) that is conjugated directly or indirectly to a second
molecule, such as a nucleic acid molecule, to facilitate detection
of the second molecule. The person of ordinary skill in the art is
familiar with detectable markers for labeling nucleic acid
molecules and their use. For example, the detectable marker can be
capable of detection by ELISA, spectrophotometry, flow cytometry,
or microscopy. Specific, non-limiting examples of detectable
markers include fluorophores, fluorescent proteins,
chemiluminescent agents, enzymatic linkages, radioactive isotopes
and heavy metals or compounds. In several embodiments, the
detectable markers are designed for use with qPCR, such as
multiplex qPCR. Various methods of labeling nucleic acid molecules
are known in the art and may be used.
[0049] Diagnosis: The process of identifying a disease by its
signs, symptoms and results of various tests. The conclusion
reached through that process is also called "a diagnosis." Forms of
testing commonly performed include blood tests, medical imaging,
urinalysis, and biopsy.
[0050] Human Immunodeficiency Virus (HIV): A retrovirus that causes
immunosuppression in humans (HIV disease), and leads to a disease
complex known as the acquired immunodeficiency syndrome (AIDS).
"HIV disease" refers to a well-recognized constellation of signs
and symptoms (including the development of opportunistic
infections) in persons who are infected by an HIV virus, as
determined by antibody or western blot studies. Laboratory findings
associated with this disease include a progressive decline in T
cells. HIV includes HIV type 1 (HIV-1) and HIV type 2 (HIV-2).
Related viruses that are used as animal models include simian
immunodeficiency virus (SW), and feline immunodeficiency virus
(FIV). Treatment of HIV-1 with HAART has been effective in reducing
the viral burden and ameliorating the effects of HIV-1 infection in
infected individuals.
[0051] HXB2 numbering system: A reference numbering system for HIV
protein and nucleic acid sequences, using the HIV-1 HXB2 strain
sequences as a reference for all other HIV-1 strain sequences. The
person of ordinary skill in the art is familiar with the HXB2
numbering system, and this system is set forth in "Numbering
Positions in HIV Relative to HXB2CG," Bette Korber et al., Human
Retroviruses and AIDS 1998: A Compilation and Analysis of Nucleic
Acid and Amino Acid Sequences. Korber B, Kuiken C L, Foley B, Hahn
B, McCutchan F, Mellors J W, and Sodroski J, Eds. Theoretical
Biology and Biophysics Group, Los Alamos National Laboratory, Los
Alamos, N. Mex., which is incorporated by reference herein in its
entirety. HXB2 is also known as: HXBc2, for HXB clone 2; HXB2R, in
the Los Alamos HIV database, with the R for revised, as it was
slightly revised relative to the original HXB2 sequence; and HXB2CG
in GENBANK.TM., for HXB2 complete genome. The HIV-1 numbering used
herein (e.g., the numbering for mutant alleles of HIV-1) is
relative to the HXB2 numbering scheme.
[0052] Hybridization: The terms "annealing" and "hybridization"
refer to the formation of base pairs between complementary regions
of DNA, RNA, or between DNA and RNA of nucleic acids. Examples of
annealing and hybridization include formation of base pairs between
two separate nucleic acid molecules, as well as formation of base
pairs between nucleic acids on a single nucleic acid molecule.
[0053] In some examples, hybridization is between two complementary
nucleic acid sequences, for example nucleic acid sequences that are
at least 90% complementary to each other, such as at least 91%,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% complementary to
each other.
[0054] In additional embodiments, hybridization conditions
resulting in particular degrees of stringency and specificity will
vary depending upon the nature of the hybridization method and the
composition and length of the hybridizing nucleic acid sequences.
Generally, the temperature of hybridization and the ionic strength
(such as the Na.sup.+ concentration) of the hybridization buffer
will determine the stringency of hybridization. Calculations
regarding hybridization conditions for attaining particular degrees
of stringency are discussed in, e.g., Sambrook et al. (Molecular
Cloning: A Laboratory Manual, 4.sup.th ed, Cold Spring Harbor, N.
Y., 2012) and Ausubel et al. (In Current Protocols in Molecular
Biology, John Wiley & Sons, New York, through supplement 104,
2013). The following is an exemplary set of hybridization
conditions and is not limiting:
Very High Stringency (Detects Sequences that Share at Least 90%
Identity) Hybridization: 5.times.SSC at 65.degree. C. for 16 hours
Wash twice: 2.times.SSC at room temperature (RT) for 15 minutes
each Wash twice: 0.5.times.SSC at 65.degree. C. for 20 minutes each
High Stringency (Detects Sequences that Share at Least 80%
Identity) Hybridization: 5.times.-6.times.SSC at 65.degree.
C.-70.degree. C. for 16-20 hours Wash twice: 2.times.SSC at RT for
5-20 minutes each Wash twice: 1.times.SSC at 55.degree.
C.-70.degree. C. for 30 minutes each Low Stringency (Detects
Sequences that Share at Least 50% Identity) Hybridization:
6.times.SSC at RT to 55.degree. C. for 16-20 hours Wash at least
twice: 2.times.-3.times.SSC at RT to 55.degree. C. for 20-30
minutes each.
[0055] In some embodiments, the probes and primers disclosed herein
can hybridize to nucleic acid molecules under low stringency, high
stringency, and very high stringency conditions.
[0056] Inhibiting or treating a disease: Inhibiting the full
development of a disease or condition, for example, in a subject
who is at risk for a disease such as HIV. "Treatment" refers to a
therapeutic intervention that ameliorates a sign or symptom of a
disease or pathological condition after it has begun to develop.
The term "ameliorating," with reference to a disease or
pathological condition, refers to any observable beneficial effect
of the treatment. The beneficial effect can be evidenced, for
example, by a delayed onset of clinical symptoms of the disease in
a susceptible subject, a reduction in severity of some or all
clinical symptoms of the disease, a slower progression of the
disease, a reduction in viral titer, an improvement in the overall
health or well-being of the subject, or by other parameters well
known in the art that are specific to the particular disease. A
"prophylactic" treatment is a treatment administered to a subject
who does not exhibit signs of a disease or exhibits only early
signs for the purpose of decreasing the risk of developing
pathology.
[0057] Isolated: An "isolated" biological component (such as a
nucleic acid molecule or protein) has been substantially separated
or purified away from other biological components in the cell of
the organism in which the component naturally occurs. The term
"isolated" does not require absolute purity. Nucleic acids and
proteins that have been "isolated" include nucleic acids and
proteins purified by standard purification methods. The term also
embraces nucleic acids and proteins prepared by recombinant
expression in a host cell, as well as chemically synthesized
nucleic acids.
[0058] Locked nucleic acid (LNA): A synthetic nucleic acid
analogue, incorporating "internally bridged" nucleoside analogues,
for example, 2'-4'- and 3'-4'-linked and other bicyclic sugar
modifications. LNA exhibits greater thermal stability when paired
with DNA, than do conventional DNA/DNA heteroduplexes and can be
synthesized on conventional nucleic acid synthesizing machines. LNA
molecules, and methods of synthesizing and using LNA molecules in
oligonucleotide, are known in the art and are disclosed, for
example, in the following publications: U.S. Pat. Nos. 6,316,198;
6,794,499; 7,034,133; 7,060,809; and 7,034,133; WO 98/22489; WO
98/39352; WO 99/14226; Nielsen et al., J. Chem. Soc. Perkin Trans.
1, 3423 (1997); Koshkin et al., Tetrahedron Letters 39, 4381
(1998); Singh & Wengel, Chem. Commun, 1247 (1998); and Singh et
al., Chem. Commun. 455 (1998); the contents of which are
incorporated herein by reference in their entirety.
[0059] Mismatch nucleotide: a nucleotide that is not complementary
to the corresponding nucleotide of the opposite polynucleotide
strand.
[0060] Multiplex qPCR: Amplification and detection of multiple
nucleic acid species in a single qPCR reaction. By multiplexing,
multiple target nucleic acids can be amplified in single tube. In
some examples, multiplex PCR permits the simultaneous detection of
the multiple HIV alleles, such as a drug-resistant allele and a
non-drug resistant allele, or multiple drug resistant alleles.
[0061] Mutation: Any change of a nucleic acid sequence as a source
of genetic variation. For example, mutations can occur within a
gene or chromosome, including specific changes in non-coding
regions of a chromosome, for instance changes in or near regulatory
regions of genes. Types of mutations include, but are not limited
to, base substitution point mutations (which are either transitions
or transversions), deletions, and insertions. Missense mutations
are those that introduce a different amino acid into the sequence
of the encoded protein; nonsense mutations are those that introduce
a new stop codon; and silent mutations are those that introduce the
same amino acid often with a base change in the third position of
the codon. In the case of insertions or deletions, mutations can be
in-frame (not changing the frame of the overall sequence) or frame
shift mutations, which may result in the misreading of a large
number of codons (and often leads to abnormal termination of the
encoded product due to the presence of a stop codon in the
alternative frame).
[0062] Nucleic acid: A deoxyribonucleotide or ribonucleotide
polymer, which can include analogues of natural nucleotides that
hybridize to nucleic acid molecules in a manner similar to
naturally occurring nucleotides. In a particular example, a nucleic
acid molecule is a single stranded (ss) DNA or RNA molecule, such
as a probe or primer. In another particular example, a nucleic acid
molecule is a double stranded (ds) nucleic acid, such as a target
nucleic acid. Examples of modified nucleic acids are those with
altered sugar moieties, such as a locked nucleic acid (LNA).
[0063] Nucleotide: The fundamental unit of nucleic acid molecules.
A nucleotide includes a nitrogen-containing base attached to a
pentose monosaccharide with one, two, or three phosphate groups
attached by ester linkages to the saccharide moiety.
[0064] The major nucleotides of DNA are deoxyadenosine
5'-triphosphate (dATP or A), deoxyguanosine 5'-triphosphate (dGTP
or G), deoxycytidine 5'-triphosphate (dCTP or C) and deoxythymidine
5'-triphosphate (dTTP or T). The major nucleotides of RNA are
adenosine 5'-triphosphate (ATP or A), guanosine 5'-triphosphate
(GTP or G), cytidine 5'-triphosphate (CTP or C) and uridine
5'-triphosphate (UTP or U).
[0065] Nucleotides include those nucleotides containing modified
bases, modified sugar moieties and modified phosphate backbones, as
known in the art.
[0066] Examples of modified base moieties which can be used to
modify nucleotides at any position on its structure include, but
are not limited to: 5-fluorouracil, 5-bromouracil, 5-chlorouracil,
5-iodouracil, hypoxanthine, xanthine, acetylcytosine,
5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N.about.6-sopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine,
5-methylaminomethyluracil, methoxyarninomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N6-isopentenyladenine,
uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine,
5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,
uracil-5-oxyacetic acid methylester, uracil-S-oxyacetic acid,
5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, and
2,6-diaminopurine.
[0067] Examples of modified sugar moieties which may be used to
modify nucleotides at any position on its structure include, but
are not limited to: arabinose, 2-fluoroarabinose, xylose, and
hexose, or a modified component of the phosphate backbone, such as
phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a
phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl
phosphotriester, or a formacetal or analog thereof.
[0068] Conventional notation is used herein to describe nucleotide
sequences: the left-hand end of a single-stranded nucleotide
sequence is the 5'-end; the left-hand direction of a
double-stranded nucleotide sequence is referred to as the
5'-direction. The direction of 5' to 3' addition of nucleotides to
nascent RNA transcripts is referred to as the transcription
direction. The DNA strand having the same sequence as an mRNA is
referred to as the "coding strand;" sequences on the DNA strand
having the same sequence as an mRNA transcribed from that DNA and
which are located 5' to the 5'-end of the RNA transcript are
referred to as "upstream sequences;" sequences on the DNA strand
having the same sequence as the RNA and which are 3' to the 3' end
of the coding RNA transcript are referred to as "downstream
sequences." Unless denoted otherwise, whenever a polynucleotide
sequence is represented, it will be understood that the nucleotides
are in 5' to 3' orientation from left to right.
[0069] Oligonucleotide probes and primers: A probe includes an
isolated nucleic acid (usually of 100 or fewer nucleotide residues)
attached to a detectable label or reporter molecule, which is used
to detect a complementary target nucleic acid molecule by
hybridization and detection of the label or reporter. Isolated
oligonucleotide probes (which as defined herein also include the
complementary sequence and corresponding RNA sequences) are of use
for detection of HIV sequences. Typically, probes are at least
about 10 nucleotides in length, such as at least about 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81,
82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
99, or about 100 nucleotides in length. For example, a probe can be
about 10-100 nucleotides in length, such as, 12-15, 12-20, 12-25,
12-30, 12-35, 12-40, 12-45, 12-50, 12-80, 14-15, 14-16, 14-18,
14-20, 14-25, 14-30, 15-16, 15-18, 15-20, 15-25, 15-30, 15-35,
15-40, 15-45, 15-50, 15-80, 16-17, 16-18, 16-20, 16-22, 16-25,
16-30, 16-40, 16-50, 17-18, 17-20, 17-22, 17-25, 17-30, 18-19,
18-20, 18-22, 18-25, 18-30, 19-20, 19-22, 19-25, 19-30, 20-21,
20-22, 20-25, 20-30, 20-35, 20-40, 20-45, 20-50, 20-80, 21-22,
21-25, 21-30, 22-25, 22-30, 22-40, 22-50, 23-24, 23-25, 23-30,
24-25, 24-30, 25-35, 25-30, 25-35, 25-40, 25-45, 25-50 or 25-80
nucleotides in length.
[0070] Primers are nucleic acid molecules, usually DNA
oligonucleotides of about 10-50 nucleotides in length (longer
lengths are also possible). Typically, primers are at least about
10 nucleotides in length, such as at least about 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,
49 or about 50 nucleotides in length. For example, a primer can be
about 10-50 nucleotides in length, such as, 12-15, 12-20, 12-25,
12-30, 12-35, 12-40, 12-45, 12-50, 14-15, 14-16, 14-18, 14-20,
14-25, 14-30, 15-16, 15-18, 15-20, 15-25, 15-30, 15-35, 15-40,
15-45, 15-50, 16-17, 16-18, 16-20, 16-22, 16-25, 16-30, 16-40,
16-50, 17-18, 17-20, 17-22, 17-25, 17-30, 18-19, 18-20, 18-22,
18-25, 18-30, 19-20, 19-22, 19-25, 19-30, 20-21, 20-22, 20-25,
20-30, 20-35, 20-40, 20-45, 20-50, 21-22, 21-25, 21-30, 22-25,
22-30, 22-40, 22-50, 23-24, 23-25, 23-30, 24-25, 24-30, 25-30,
25-35, 25-40 or 25-45, 25-50 nucleotides in length.
[0071] Probes and primers can also be of a maximum length, for
example no more than 15, 25, 25, 40, 50, 75 or 100 nucleotides in
length.
[0072] Primers may be annealed to a complementary target DNA strand
by nucleic acid hybridization to form a hybrid between the primer
and the target DNA strand, and then extended along the target DNA
strand by a DNA polymerase enzyme. One of skill in the art will
appreciate that the hybridization specificity of a particular probe
or primer typically increases with its length. Thus, for example, a
probe or primer including 20 consecutive nucleotides typically will
anneal to a target with a higher specificity than a corresponding
probe or primer of only 15 nucleotides. In some embodiments, probes
and primers are used in combination in a qPCR reaction.
[0073] Plus Primer: An oligonucleotide primer for use in
allele-specific PCR. A plus primer includes a locked nucleic acid
at the 3' position that is complementary to a mutant allele of a
target nucleic acid, and a mismatch nucleotide at the -1 position
from the 3' end that is not complementary to the target nucleic
acid molecule.
[0074] Primer pair: Two primers (one "forward" and one "reverse")
that can be used for amplification of a nucleic acid sequence, for
example by polymerase chain reaction (PCR) or other in vitro
nucleic-acid amplification methods. The forward and reverse primers
of a primer pair do not hybridize to overlapping complementary
sequences on the target nucleic acid sequence.
[0075] Polymorphism: A variation in a gene sequence. The
polymorphisms can be those variations (DNA sequence differences,
e.g., substitutions, deletions, or insertions) which are generally
found between individuals or different ethnic groups and geographic
locations which, while having a different sequence, produce
functionally equivalent gene products. The term can also refer to
variants in the sequence which can lead to gene products that are
not functionally equivalent and/or have altered function.
Polymorphisms also encompass variations which can be classified as
alleles and/or mutations which either produce no gene product or an
inactive gene product or an active gene product produced at an
abnormal rate or in an inappropriate tissue or in response to an
inappropriate stimulus. Alleles are the alternate forms that occur
at the polymorphism. In one non-limiting example, a polymorphism is
a mutation that confers resistance to a particular drug, for
example, a HIV-1 therapeutic.
[0076] Polymorphisms can be referred to, for instance, by the
nucleotide position at which the variation exists, by the change in
amino acid sequence caused by the nucleotide variation, or by a
change in some other characteristic of the nucleic acid molecule or
protein that is linked to the variation.
[0077] Proof-Reading Polymerase: A polymerase enzyme with 3' to 5'
exonuclease activity. A Non-limiting example of a proof-reading
polymerase include Taq polymerase. Proof-reading polymerases with
3' to 5' exonuclease activity are known to the person of ordinary
skill in the art and are commercially available, for example, from
New England Biolabs, Ipswich, Mass.
[0078] Real-Time PCR (qPCR): A method for detecting and measuring
products generated during each cycle of a PCR, which are
proportionate to the amount of template nucleic acid prior to the
start of PCR. The information obtained, such as an amplification
curve, can be used to determine the presence of a target nucleic
acid (such as a HIV nucleic acid or polymorphism thereof) and/or
quantitate the initial amounts of a target nucleic acid sequence.
Exemplary procedures for qPCR can be found in "Quantitation of
DNA/RNA Using Real-Time PCR Detection" published by Perkin Elmer
Applied Biosystems (1999); PCR Protocols (Academic Press, New York,
1989); A-Z of Quantitative PCR, Bustin (ed.), International
University Line, La Jolla, Calif., 2004; and Quantitative Real-Time
PCR in Applied Microbiology, Filion (Ed), Caister Academic Press,
2012.
[0079] In some examples, the amount of amplified target nucleic
acid (for example a HIV nucleic acid) is detected using a labeled
probe, such as a probe labeled with a fluorophore, for example a
TAQMAN.RTM. probe. In other examples, the amount of amplified
target nucleic acid (for example a HIV nucleic acid) is detected
using a DNA intercalating dye. The increase in fluorescence
emission is measured in real-time, during the course of the qPCR.
This increase in fluorescence emission is directly related to the
increase in target nucleic acid amplification. In some examples,
the change in fluorescence (Delta Rn; dRn; .DELTA.Rn) is calculated
using the equation dRn=Rn.sup.+-Rn.sup.-, with Rn.sup.+ being the
fluorescence emission of the product at each time point and
Rn.sup.- being the fluorescence emission of the baseline. The dRn
values are plotted against cycle number, resulting in amplification
plots for each sample. The threshold cycle (Ct) is the PCR cycle
number at which the fluorescence emission (dRn) exceeds a chosen
threshold, which is typically 10 times the standard deviation of
the baseline (this threshold level can, however, be changed if
desired).
[0080] The threshold cycle is when the system begins to detect the
increase in the signal associated with an exponential growth of PCR
product during the log-linear phase. This phase provides
information about the reaction. The slope of the log-linear phase
is a reflection of the amplification efficiency. The efficiency of
the reaction can be calculated by the following equation:
E=10.sup.(-1/slope) for example. The efficiency of the PCR should
be 90-100% meaning doubling of the amplicon at each cycle. This
corresponds to a slope of -3.1 to -3.6 in the C.sub.t vs.
log-template amount standard curve.
[0081] Recombinant: A recombinant nucleic acid is one that has a
sequence that is not naturally occurring or has a sequence that is
made by an artificial combination of two otherwise separated
segments of sequence. This artificial combination can be
accomplished by chemical synthesis or, more commonly, by the
artificial manipulation of isolated segments of nucleic acids,
e.g., by genetic engineering techniques.
[0082] Sensitivity and specificity: Statistical measurements of the
performance of a binary classification test. Sensitivity measures
the proportion of actual positives which are correctly identified
(e.g., the percentage of samples that are identified as including
nucleic acid from a particular virus). Specificity measures the
proportion of negatives which are correctly identified (e.g., the
percentage of samples that are identified as not including nucleic
acid from a particular virus).
[0083] Sequence identity: The similarity between two nucleic acid
sequences is expressed in terms of the similarity between the
sequences, otherwise referred to as sequence identity. Sequence
identity is frequently measured in terms of percentage identity,
similarity, or homology; a higher percentage identity indicates a
higher degree of sequence similarity.
[0084] The NCBI Basic Local Alignment Search Tool (BLAST), Altschul
et al., J. Mol. Biol. 215:403-10, 1990, is available from several
sources, including the National Center for Biotechnology
Information (NCBI, Bethesda, Md.), for use in connection with the
sequence analysis programs blastp, blastn, blastx, tblastn and
tblastx. It can be accessed through the NCBI website. A description
of how to determine sequence identity using this program is also
available on the website.
[0085] When less than the entire sequence is being compared for
sequence identity, homologs will typically possess at least 75%
sequence identity over short windows of 10-20 amino acids, and can
possess sequence identities of at least 85% or at least 90% or 95%
depending on their similarity to the reference sequence. Methods
for determining sequence identity over such short windows are
described on the NCBI website.
[0086] These sequence identity ranges are provided for guidance
only; it is entirely possible that strongly significant homologs
could be obtained that fall outside of the ranges provided.
[0087] An alternative indication that two nucleic acid molecules
are closely related is that the two molecules hybridize to each
other under stringent conditions. Stringent conditions are
sequence-dependent and are different under different environmental
parameters. Generally, stringent conditions are selected to be
about 5.degree. C. to 20.degree. C. lower than the thermal melting
point (Tm) for the specific sequence at a defined ionic strength
and pH. The Tm is the temperature (under defined ionic strength and
pH) at which 50% of the target sequence hybridizes to a perfectly
matched probe. Conditions for nucleic acid hybridization and
calculation of stringencies can be found in Sambrook et al.; and
Tijssen, Hybridization With Nucleic Acid Probes, Part I: Theory and
Nucleic Acid Preparation, Laboratory Techniques in Biochemistry and
Molecular Biology, Elsevier Science Ltd., 1993.
[0088] Signal: A detectable change or impulse in a physical
property that provides information. In the context of the disclosed
methods, examples include electromagnetic signals such as light,
for example light of a particular quantity or wavelength. In
certain examples, the signal is the disappearance of a physical
event, such as quenching of light.
[0089] Single nucleotide polymorphism (SNP): The polynucleotide
sequence variation present at a single nucleotide residue within
different alleles of the same genomic sequence. This variation may
occur within the coding region or non-coding region (i.e., in the
promoter region) or an intergenic (between genes) sequence of a
genomic sequence. Detection of one or more SNP allows
differentiation of different alleles of a single genomic sequence.
Most common SNPs have only two alleles.
[0090] SNPs within a coding sequence will not necessarily change
the amino acid sequence of the protein that is produced, due to
degeneracy of the genetic code. A SNP in which both forms lead to
the same polypeptide sequence is termed "synonymous" (sometimes
called a silent mutation)--if a different polypeptide sequence is
produced they are "nonsynonymous". A nonsynonymous change may
either be missense or "nonsense", where a missense change results
in a different amino acid, while a nonsense change results in a
premature stop codon.
[0091] Subject: Any mammal, such as humans, non-human primates,
pigs, sheep, cows, rodents and the like. In two non-limiting
examples, a subject is a human subject or a murine subject. Thus,
the term "subject" includes both human and veterinary subjects. A
immunocompromised subject is a subject with a suppressed immune
system, such as a subject with HIV.
[0092] Target nucleic acid molecule: A nucleic acid molecule whose
detection, quantitation, qualitative detection, or a combination
thereof, is intended. The nucleic acid molecule need not be in a
purified form. Various other nucleic acid molecules can also be
present with the target nucleic acid molecule. For example, the
target nucleic acid molecule can be a specific nucleic acid
molecule (which can include RNA or DNA), the amplification of which
is intended. In some examples, a target nucleic acid includes a
region of the HIV genome that includes an allele specific mutation
that results in drug resistance. Purification or isolation of the
target nucleic acid molecule, if needed, can be conducted by
methods known to those in the art, such as by using a commercially
available purification kit or the like.
[0093] Under conditions sufficient for: A phrase that is used to
describe any environment that permits a desired activity. In one
example the desired activity is amplification of a nucleic acid
molecule.
[0094] Wild-type: The genotype or phenotype that is most prevalent
in nature. The naturally occurring, non-mutated version of a
nucleic acid sequence. Among multiple alleles, the allele with the
greatest frequency within the population is usually the wild-type.
The term "native" can be used as a synonym for "wild-type."
II. Detecting Alleles of a Nucleic Acid Molecule
[0095] A method is disclosed for detecting alleles of a target
nucleic acid molecule using a novel allele-specific PCR (ASPCR)
assay. The methods are useful, for example, for identifying and
diagnosing a subject with a particular polymorphism, such as a drug
resistant allele of HIV-1.
[0096] The principle of ASPCR is based on the differences of
amplification efficiencies using mutation-specific and wt-specific
oligonucleotide primers in a qPCR assay with a common target
nucleic acid template from a biological sample. The resulting
"test" amplification is compared with a "control" amplification
that detects total amount of the target template in the biological
sample to normalize the amplification assay. The difference between
the cycle number when the test amplification reaches a threshold
amount of amplified DNA, and the cycle number when the control
amplification reached the threshold amount of amplified DNA is the
.DELTA.Ct value for the ASPCR assay. The .DELTA.Ct value for the
ASPCR assay can be compared to a standard control (or curve)
generated using a mixture of target nucleic acid molecules
comprising a pre-selected proportion of the mutant and wildtype
first alleles to detect the mutant first allele of the target
nucleic acid molecule in the biological sample.
[0097] The disclosed ASPCR assay includes use of one or more "Plus"
primers, which include a penultimate mismatch at the -1 position
from the 3' end, and a locked nucleic acid (LNA) at the 3' end that
complements with an allele of interest in the target nucleic acid.
As illustrated in Example 1, use of the Plus primers increases the
difference in amplification efficiency between Mutant and Wild Type
by 3-5 cycles as calculated by qPCR; thereby increasing selectivity
and sensitivity of amplification for the allele of interest.
[0098] The disclosed ASPCR assay utilizes improved methods of
normalizing the amount of target nucleic acid molecules in a
biological sample to provide for increased sensitivity of the
assay. In several embodiments the method includes a control qPCR
assay utilizing a mixture of primers for at least one half of the
primer pair (the forward primer set) used for the ASPCR assay, as
follows:
[0099] A) two primers: a plus primer (including a 3' LNA specific
for the allele of interest and a mismatch at the -1 position) and a
corresponding control primer (including a 3' LNA specific for the
wild-type sequence and the same mismatch at the -1 position). The
plus and the control primers are identical except for the '3 end
position (which is specific for the allele of interest in the Plus
primer and specific for wild-type sequence in the control primer);
or
[0100] B) four primers: a plus primer (including a 3' LNA specific
for the allele of interest and a mismatch at the -1 position), and
three additional primers, including the remaining other nucleotides
as LNAs at the 3' end, and the same mismatch at the -1 position.
The four primers are identical except for the '3 end position.
[0101] The remaining (reverse) half of the primer pair for the
normalization qPCR assay includes either a single primer having a
sequence common to both wild-type and mutant allelic DNA, or in the
case of a ASPCR assay that can detect two alleles, the remaining
half for the normalization qPCR assay can include two or four
primers as described above that are complementary to the second
allele targeted by the linked ASPCR assay. Using these primer
mixtures, a standard curve can be generated by measuring the Delta
Ct between the ASPCR and the Total-PCR of a series of standard
templates, for example ranging from 0.01% mixtures of
mutant/wild-type up to 100% mutant. As illustrated in Example 1,
the novel control amplification provides for improved sensitivity
and specificity compared to prior control amplification
reactions.
[0102] In some embodiments, the disclosed methods can predict with
a sensitivity of at least 90% and/or a specificity of at least 90%
for the identity of a mutant allele of a nucleic acid molecule in a
biological sample, such as a sensitivity of at least 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or even 100% and a specificity of at
least of at least 91%, 292%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
even 100%.
[0103] In further embodiments, the disclosed methods can detect the
proportion (such as no more than 20%, for example, no more than
15%, no more than 10%, no more than 5%, no more than 4%, no more
than 3%, no more than 2%, no more than 1%, no more than 0.1%, or
less) of target nucleic acid molecules in a biological sample
including a mutant allele of interest.
[0104] In several embodiments, a method of detecting a first allele
of a target nucleic acid molecule in a biological sample is
provided. The method includes a test amplification and a control
amplification. The test amplification includes amplifying the
target nucleic acid molecule from the biological sample by qPCR
using a test primer pair comprising (1) a first plus primer
comprising a locked nucleic acid at the 3' end that is
complementary to the first allele, a mismatch nucleotide at the -1
position from the 3' end, and remaining nucleotides complementary
to the target nucleic acid molecule, and (2) a reverse primer of
the test primer pair. The control amplification includes amplifying
the target nucleic acid molecule from the biological sample by qPCR
using a control set of primers comprising (1) the first primer
pair, and (2) a first control primer comprising a locked nucleic
acid at the 3' end that is complementary to the first allele, and
remaining nucleotides the same as the first plus primer. The Ct
value of the test amplification and the Ct value of the control
amplification are measured, and the difference between the Ct
values (.DELTA.Ct) is determined. The .DELTA.Ct value for the ASPCR
assay can be compared to a standard curve generated using known
mixtures of mutant and wild-type target nucleic acid molecules to
determine the proportion of the mutant and/or wild-type allele of
the target nucleic acid molecule in the biological sample.
[0105] In additional embodiments, the control set of primers can
further include additional control primers. For example, the
control amplification can include a third control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype first allele, and remaining
nucleotides that are the same as the first plus primer; and a
fourth control primer, comprising a locked nucleic acid at the 3'
end that is not complementary to the mutant or wildtype first
allele and is not the same as the locked nucleic acid of the third
control primer, and remaining nucleotides that are the same as the
first plus primer. The additional control primers provide increase
sensitivity to the ASPCR assay.
[0106] In other embodiments, the assay can be used to detect a
second allele of the target nucleic acid molecule in the biological
sample. For example, the ASPCR can be used to detect two linked
drug-resistance alleles of the target nucleic acid molecule. In
some such embodiments, the reverse primer of the test primer pair
can be a second plus primer comprising a locked nucleic acid at the
3' end that is complementary to the mutant second allele, a
mismatch nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule. Further, the control set of primers includes a second
control primer comprising a locked nucleic acid at the 3' end that
is complementary to a wildtype second allele corresponding to the
mutant second allele, and remaining nucleotides that are the same
as the second plus primer. In such assays, the difference between
the Ct values of the test and control amplifications are compared
with a standard control generated using a mixture of target nucleic
acid molecules comprising a pre-selected proportion of the mutant
and wildtype first alleles and the mutant and wildtype second
alleles to detect the mutant first and second alleles of the target
nucleic acid molecule in the biological sample
[0107] In additional embodiments including detection of two alleles
of the target nucleic acid molecule, the control set of primers can
further include additional control primers. For example, the
control set of primers can include a third control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype first allele, and remaining
nucleotides that are the same as the first plus primer, as well as
a fourth control primer, comprising a locked nucleic acid at the 3'
end that is not complementary to the mutant or wildtype first
allele and is not the same as the locked nucleic acid of the third
control primer, and remaining nucleotides that are the same as the
first plus primer. Optionally, the control set of primers can
further include a fifth control primer, comprising a locked nucleic
acid at the 3' end that is not complementary to the mutant or
wildtype second allele, and remaining nucleotides that are the same
as the second plus primer, as well as a sixth control primer,
comprising a locked nucleic acid at the 3' end that is not
complementary to the mutant or wildtype second allele and is not
the same as the locked nucleic acid of the fifth control primer,
and remaining nucleotides that are the same as the second plus
primer. The additional control primers provide increase sensitivity
to the ASPCR assay.
[0108] In some embodiments, a non-proof-reading polymerase (e.g.,
Taq polymerase) can be used in the test and/or control
amplification steps of the disclosed methods.
[0109] In additional embodiments, the assay can include a first
round amplification of template DNA from the biological sample
prior to the test or control amplifications, wherein the first
round amplification comprises use of a proof-reading DNA polymerase
(e.g., Phusion polymerase, sold by New England Biolabs). The
product of the first round amplification is then used as template
for the test and control amplifications as described herein.
A. Detecting HIV Alleles
[0110] Even though treatment of HIV infections with antiretroviral
(ARV) drugs has improved the clinical outcomes of HIV-1 infected
patients considerably, their efficacy is still limited, due to the
development and transmission of HIV-1 drug-resistant variants. High
replication rates (i.e. production of >109 virions per day)
coupled to the error-prone nature of HIV-1 Reverse Transcriptase
(RT), frequently leads to the production of randomly generated
mutations and a population of HIV-1 variants within a patient
commonly referred to as the "quasispecies." Furthermore, some of
these randomly generated mutations can confer high level drug
resistance to certain drugs (i.e. lamivudine, efavirenz, or
nevirapine) by means of a single nucleotide substitution within the
viral genome. These HIV resistance variants are believed to
preexist even prior to the initiation of drug therapy and are
usually the first to appear during virologic failure under
treatment. In contrast, resistance to other antiretroviral drugs
such as protease inhibitors and/or combination therapies, requires
the accumulation of multiple mutations on the HIV genome.
[0111] Accordingly, in several embodiments the disclosed methods
are utilized for detection of one or more alleles of HIV, such as a
mutant allele of HIV-1 or HIV-2 that confers drug resistance. In
some embodiments, the methods are used to detect one or more mutant
alleles of HIV-1 reverse transcriptase. An exemplary nucleic acid
sequence encoding a wild-type HIV-1 reverse transcriptase (HXB2
strain) is set forth as SEQ ID NO: 32:
TABLE-US-00001 cccattagccctattgagactgtaccagtaaaattaaagccaggaatgga
tggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcat
tagtagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaatt
gggcctgaaaatccatacaatactccagtatttgccataaagaaaaaaga
cagtactaaatggagaaaattagtagatttcagagaacttaataagagaa
ctcaagacttctgggaagttcaattaggaataccacatcccgcagggtta
aaaaagaaaaaatcagtaacagtactggatgtgggtgatgcatatttttc
agttcccttagatgaagacttcaggaagtatactgcatttaccataccta
gtataaacaatgagacaccagggattagatatcagtacaatgtgcttcca
cagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaat
cttagagccttttagaaaacaaaatccagacatagttatctatcaataca
tggatgatttgtatgtaggatctgacttagaaatagggcagcatagaaca
aaaatagaggagctgagacaacatctgttgaggtggggacttaccacacc
agacaaaaaacatcagaaagaacctccattcctttggatgggttatgaac
tccatcctgataaatggacagtacagcctatagtgctgccagaaaaagac
agctggactgtcaatgacatacagaagttagtggggaaattgaattgggc
aagtcagatttacccagggattaaagtaaggcaattatgtaaactcctta
gaggaaccaaagcactaacagaagtaataccactaacagaagaagcagag
ctagaactggcagaaaacagagagattctaaaagaaccagtacatggagt
gtattatgacccatcaaaagacttaatagcagaaatacagaagcaggggc
aaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaa
acaggaaaatatgcaagaatgaggggtgcccacactaatgatgtaaaaca
attaacagaggcagtgcaaaaaataaccacagaaagcatagtaatatggg
gaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaaca
tggtggacagagtattggcaagccacctggattcctgagtgggagtttgt
taatacccctcccttagtgaaattatggtaccagttagagaaagaaccca
tagtaggagcagaaaccttctatgtagatggggcagctaacagggagact
aaattaggaaaagcaggatatgttactaatagaggaagacaaaaagttgt
caccctaactgacacaacaaatcagaagactgagttacaagcaatttatc
tagctttgcaggattcgggattagaagtaaacatagtaacagactcacaa
tatgcattaggaatcattcaagcacaaccagatcaaagtgaatcagagtt
agtcaatcaaataatagagcagttaataaaaaaggaaaaggtctatctgg
catgggtaccagcacacaaaggaattggaggaaatgaacaagtagataaa
ttagtcagtgctggaatcaggaaagtacta
[0112] An exemplary amino acid sequence of a wild-type HIV-1
reverse transcriptase (HXB2 strain, p66 subunit) is set forth as
SEQ ID NO: 36:
TABLE-US-00002 PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK LVSAGIRKVL
[0113] Several drug resistant HIV-1 mutations are known to the
person of ordinary skill in the art, see, e.g., Johnson et al.,
"Update of the drug resistance mutations in HIV-1: March 2013", Top
Antivir Med. 21(1):6-14, 2013, which is incorporated by reference
herein in its entirety. Further updates to the list of drug
resistant HIV-1 mutations can be found at www.iasusa.org. Exemplary
drug resistant HIV-1 mutations include, but are not limited to, the
following mutant alleles of HIV-1 reverse transcriptase: K65R,
M184V, M184I, M41L, A62V, K65N, K65E, D67N, D67G, D67E, T69I, T69D,
K70R, K70E, K70G, K70T, K70N, K70Q, L74V, L74I, V75I, V75M, V75T,
F77L, L100I, K101P, K103N, K103S, V106M, Y115F, F116Y, Q151M,
Y181C, Y181I, Y188L, G190S, G190A, L210W, T215Y, T215F, T215E,
T215I, T215C, T215D, K219Q, K219E, K219N, K219R, P225H, or M230L
(numbering according to HXB2 numbering system). The disclosed
methods can be used to detect one or more (e.g., two) of these
mutant alleles of HIV-1 reverse transcriptase in a biological
sample. In some embodiments, the methods can be used to detect a
first allele and a second allele of HIV-1 or HIV-2, in a single
qPCR assay. For example, a first allele and a second allele
selected from one of K65R and M184V, K65R and M184I, K65R and
K103N, K70E and M184V, K70E and M184I, K70E and K103N, K103N and
M184V, or K103N and M184I.
[0114] Administration of tenofovir and emtricitabine (Truvada.RTM.)
is the most commonly prescribed combination drug for HIV, with
estimated annual sales of $2.4 billion dollars. Tenofovir
resistance can develop by the K65R or K70E mutations, and
emtricitabine resistance by M184V/I of which all involve single
nucleotide changes in HIV RT gene. Accordingly, in some
embodiments, the disclosed methods can be applied to assess
resistant mutations to combination therapy with tenofovir and
emtricitabine. Additionally, the linked HIV-1 RT K103N and Y181C
mutations can confer resistance to non-nucleoside reverse
transcriptase inhibitors (NNRTIs), and, in some embodiments, the
disclosed methods can be applied to assess these resistant
mutations to NNRTI therapy.
[0115] Exemplary oligonucleotide primers for use in the disclosed
methods of detecting one or more mutant alleles of HIV-1 reverse
transcriptase are provided in Table 1.
TABLE-US-00003 TABLE 1 Exemplary target nucleic acids and alleles,
Plus primers, and control primers for targeting alleles of HIV-1
Reverse Transcriptase Wild-type specific Plus primer Control/Total
Allele-specific primer sequence Additional control Exemplary
reverse/ Plus Primer (with LNA at 3'end primers (when forward
primer sequence (com- that is complemen- using three or for PCR
assay (does plementary to tary to wild-type four control not need
to be for Allele mutant sequence) allele sequence) primers are
used) linked PCR assays) a K65R CTCCARTATTTGC CTCCARTATTTGC
CTCCARTATTT TATTCCTAATTGAA CATAAAA + G CATAAAA + A GCCATAAAA +
CYTCCCA (SEQ ID NO: 1) (SEQ ID NO: 2) C (SEQ ID NO: 3)
CTCCAATATTTGC CTCCAATATTTG (SEQ ID NO: 33) TATTCCTAATTGAA CATAAAA +
G CCATAAAA + A CTCCARTATTT CCTCCCA (SEQ ID NO: 39) (SEQ ID NO: 41)
GCCATAAAA + (SEQ ID NO: 37) CTCCAGTATTTGC CTCCAGTATTTG T
TATTCCTAATTGAA CATAAAA + G CCATAAAA + A (SEQ ID NO: 34) CTTCCCA
(SEQ ID NO: 40) (SEQ ID NO: 42) CTCCAATATTT (SEQ ID NO: 38)
GCCATAAAA + C (SEQ ID NO: 43) CTCCAATATTT GCCATAAAA + T (SEQ ID NO:
44) CTCCAGTATTT GCCATAAAA + C (SEQ ID NO: 45) CTCCAGTATTT GCCATAAAA
+ T (SEQ ID NO: 46) b K70E GCCATAAAAAAG GCCATAAAAAAG TATTCCTAATTGAA
AAGGACCAGTA + AAGGACCAGTA + CYTCCCA G A (SEQ ID NO: 3) (SEQ ID NO:
4) (SEQ ID NO: 5) c M184 CTAAGTCAGATCC CTAAGTCAGATC TAGTATAAACAAT V
TACATACAAGTCA CTACATACAAGT GAGACACCAGGGA TCC + C CATCC + T TTA (SEQ
ID NO: 6) (SEQ ID NO: 7) (SEQ ID NO: 8) d M184I CCCTATTTCTAAG
CCCTATTTCTAA TAGTATAAACAAT TCAGATCCTACAT GTCAGATCCTAC GAGACACCAGGGA
ACAAAGTCAT + T ATACAAAGTCAT TTA (SEQ ID NO: 9) + C (SEQ ID NO: 8)
(SEQ ID NO: 10) e K103N CCCACATCTAGTA CCCACATCTAGT CCCACATCTAG
AAGTGGAGAAAAT CTGTCACTGATT + ACTGTCACTGAT TACTGTCACTG TAGTAGATTTCAG
A T + T ATT + C GGA (SEQ ID NO: 11) (SEQ ID NO: 12) (SEQ ID NO: 13)
(SEQ ID NO: 14) CCCACATCTAG TACTGTCACTG ATT/ + G (SEQ ID NO: 15) f
K103N CCCACATCTAGTA CCCACATCTAGT CCCACATCTAG AAGTGGAGAAAAT
CTGTCACTGATT + ACTGTCACTGAT TACTGTCACTG TAGTAGATTTCAG G T + T ATT +
C GGA (SEQ ID NO: 15) (SEQ ID NO: 12) (SEQ ID NO: 13) (SEQ ID NO:
14) CCCACATCTAG TACTGTCACTG ATT + A (SEQ ID NO: 11) g Y181C
CTACATACAAGTC CTACATACAAGT CACCAGGGATTAG ATCCATATATTG +
CATCCATATATT ATATCAATATAAT C G + T GTG (SEQ ID NO: 16) (SEQ ID NO:
17) (SEQ ID NO: 18) h G190A CTATGTTGCCCTA CTATGTTGCCCT
CACCAGGGATTAG TTTCTAAGTCAGA ATTTCTAAGTCA ATATCAATATAAT + G GA + C
GTG (SEQ ID NO: 19) (SEQ ID NO: 20) (SEQ ID NO: 18)
In Table 1, underlined nucleic acids indicate the penultimate
mismatch, and a nucleic acid following a "+" is a locked nucleic
acid (LNA). In Table 1, several sequences include an "R"
nucleotide, including SEQ ID NOs: 1, 2, 33, and 34. The "R"
indicates that the particular position of the nucleic acid molecule
can be adenine or guanine. For reference, corresponding sequences
with "A" or "G" nucleotides are shown as SEQ ID NOs: 39-46.
Additionally, SEQ ID NO: 3 includes a "Y" nucleic acid. The "Y"
indicates that the particular position of the nucleic acid molecule
can be cytosine or thymine. For reference, corresponding sequences
with "C" or "T" nucleotides are shown as SEQ ID NOs: 37-38. The
person of skill in the art will appreciate that amplification
assay
[0116] In some embodiments of the disclosed method, the test
amplification and the control amplification include use of a first
plus primer, a reverse primer, and a first control primer as listed
in one of the rows of Table 1. In additional embodiments, the test
amplification and/or the control amplification include use of a
first plus primer, a reverse primer, a first control primer, and an
additional control primer as listed in one of the rows of Table
1.
[0117] In other embodiments, the method comprises detecting a K65R
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 1, 2, and 3, respectively. In these assays, SEQ ID NOs: 1
and 2 can be substituted with SEQ ID NOs: 29 and 41, or SEQ ID NOs:
40 and 42. Further, SEQ ID NO 3 can be substituted with SEQ ID NOs:
37 or 38. In some such assays, additional control primers can be
added to the amplification assay, for example SEQ ID NOs: 33 and 34
can be added to the assay.
[0118] In other embodiments, the method comprises detecting a K65R
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 39 and 41, and 3 (or SEQ ID NOs: 37 or 38), respectively,
and additional control primers can be included in the assay, such
as SEQ ID NOs: 43 and 44.
[0119] In other embodiments, the method comprises detecting a K65R
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 40 and 42, and 3 (or SEQ ID NOs: 37 or 38), respectively,
and additional control primers can be included in the assay, such
as SEQ ID NOs: 45 and 46.
[0120] In other embodiments, the method comprises detecting a K65R
allele and a M184V allele of HIV-1 reverse transcriptase, and the
first plus primer, the first control primer, the second plus
primer, and the second control primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 1, 2, 6, and 7, respectively. In further embodiments, the
method comprises detecting a K65R and a M184I allele of HIV-1
reverse transcriptase, and the first plus primer, the first control
primer, the second plus primer, and the second control primer,
comprise, consist, or consist essentially of, the nucleic acid
sequences set forth as SEQ ID NOs: 1, 2, 9, and 10, respectively.
In these assays, SEQ ID NOs: 1 and 2 can be substituted with SEQ ID
NOs: 29 and 41, or SEQ ID NOs: 40 and 42.
[0121] In other embodiments, the method comprises detecting a K70E
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 4, 5, and 3, respectively. In these assays, SEQ ID NO 3 can
be substituted with SEQ ID NOs: 37 or 38.
[0122] In other embodiments, the method comprises detecting a M184V
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 6, 7, and 8, respectively.
[0123] In other embodiments, the method comprises detecting a M184I
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 9, 10, and 8, respectively.
[0124] In other embodiments, the method comprises detecting a K103N
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 11, 12, and 14, respectively. In some such assays,
additional control primers can be added to the amplification assay,
for example SEQ ID NOs: 13 and 15 can be added to the assay.
[0125] In other embodiments, the method comprises detecting a K103N
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 15, 12, and 14, respectively. In some such assays,
additional control primers can be added to the amplification assay,
for example SEQ ID NOs: 13 and 11 can be added to the assay.
[0126] In other embodiments, the method comprises detecting a Y181C
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 16, 17, and 18, respectively.
[0127] In other embodiments, the method comprises detecting a G190A
allele of HIV-1 reverse transcriptase, and the first plus primer,
the first control primer, the reverse primer, comprise, consist, or
consist essentially of, the nucleic acid sequences set forth as SEQ
ID NOs: 19, 20, and 18, respectively.
B. Additional Description of the Disclosed Methods
[0128] The skilled artisan will appreciate that detecting the
presence or absence (or amount or proportion) of the target nucleic
acid molecule as described herein using qPCR assays can include
detecting the target nucleic acid molecule after a particular
amplification cycle of the qPCR assay. For example, after 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and/or 50 amplification
cycles of the qPCR assay, or at least that may cycles, or no more
than that many cycles.
[0129] In several embodiments, the biological sample can be
selected from any clinical samples useful for detection of disease
or infection (e.g., HIV infection) or an allele of interest in a
subjects. Exemplary biological samples include, without limitation,
cells, cell lysates, blood smears, cytocentrifuge preparations,
cytology smears, bodily fluids (e.g., blood, plasma, serum, saliva,
sputum, urine, bronchoalveolar lavage, semen, CSF, etc.), tissue
biopsies or autopsies, fine-needle aspirates, and/or tissue
sections. In one embodiment, the biological sample is a urine
sample. In another embodiment, the biological sample is a serum
sample. In a further embodiment, the biological sample is a CSF
sample. In a particular example, a biological sample is obtained
from a subject having, suspected of having or at risk of having,
HIV; for example, a subject having HIV infection. Standard
techniques for acquisition of such samples are available (see, e.g.
Schluger et al., J. Exp. Med. 176:1327-33, 1992; Bigby et al., Am.
Rev. Respir. Dis. 133:515-18, 1986; Kovacs et al., NEJM 318:589-93,
1988; and Ognibene et al., Am. Rev. Respir. Dis. 129:929-32, 1984).
The sample can be used directly or can be processed, such as by
adding solvents, preservatives, buffers, or other compounds or
substances. In some embodiments, nucleic acids are isolated from
the sample. DNA or RNA can be extracted using standard methods. For
instance, rapid DNA preparation can be performed using a
commercially available kit (e.g., the Qiagen Tissue Kit, Qiagen,
Inc., Valencia, Calif.). The DNA preparation technique can be
chosen to yield a nucleotide preparation that is accessible to and
amenable to nucleic acid amplification.
[0130] The target nucleic acid molecule can include or consist of
at least about 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100,
150, 200, 250, 300, 350, 400, 450, 500, or more consecutive
nucleotides of a nucleic acid sequence (such as of the HIV-1
genome, e.g., HIV-1 reverse transcriptase gene).
[0131] In some embodiments, the oligonucleotide probe can be
labeled, for example with a base-linked or terminally-linked
fluorophore and non-fluorescent quencher for use in qPCR assays.
Fluorophores for use in qPCR assays are known in the art. They can
be obtained, for example, from Life Technologies (Gaithersburg,
Md.), Sigma-Genosys (The Woodlands, Tex.), Genset Corp. (La Jolla,
Calif.), or Synthetic Genetics (San Diego, Calif.). Fluorophores
can be conjugated to the oligonucleotides, for example by
post-synthesis modification of oligonucleotides that are
synthesized with reactive groups linked to bases. Useful
fluorophores include: fluorescein, fluorescein isothiocyanate
(FITC), carboxy tetrachloro fluorescein (TET), NHS-fluorescein, 5
and/or 6-carboxy fluorescein (FAM), 5-(or 6-)
iodoacetamidofluorescein, 5-{[2(and
3)-5-(Acetylmercapto)-succinyl]amino} fluorescein
(SAMSA-fluorescein), 5'-hexachloro-fluorescein (HEX),
6-carboxy-4',5'-dichloro-2',7'dimethoxyfluorescein,succinimidyl
ester (JOE) and other fluorescein derivatives, rhodamine, Lissamine
rhodamine B sulfonyl chloride, Texas red sulfonyl chloride, 5
and/or 6 carboxy rhodamine (ROX) and other rhodamine derivatives,
coumarin, 7-amino-methyl-coumarin,
7-Amino-4-methylcoumarin-3-acetic acid (AMCA), and other coumarin
derivatives, BODIPY fluorophores, Cascade Blue fluorophores such as
8-methoxypyrene-1,3,6-trisulfonic acid trisodium salt, Lucifer
yellow fluorophores such as 3,6-Disulfonate-4-amino-naphthalimide,
phycobiliproteins derivatives, Alexa fluor dyes (available from
Molecular Probes, Eugene, Oreg.) and other fluorophores known to
those of skill in the art. For a general listing of useful
fluorophores, see also Hermanson, G. T., BIOCONJUGATE TECHNIQUES
(Academic Press, San Diego, 1996).
[0132] Quenchers for use in qPCR assays are also known in the art
and include, for example, 6-carboxytetramethylrhodamine,succinidyl
ester (6-TAMRA; TAMRA) and "non-fluorescent quencher (NFP)" for use
with TAQMAN.TM. probes available from Life technologies.
[0133] Several embodiments include the use of PCR and/or qPCR. PCR
reaction conditions typically include either two or three step
cycles. Two step cycles have a denaturation step followed by a
hybridization/elongation step. Three step cycles include a
denaturation step followed by a hybridization step during which the
primer hybridizes to the strands of DNA, followed by a separate
elongation step. The polymerase reactions are incubated under
conditions in which the primers hybridize to the target sequences
and are extended by a polymerase. The amplification reaction cycle
conditions are selected so that the primers hybridize specifically
to the target sequence and are extended.
[0134] Primers for the disclosed assays are typically designed so
that all of the primers participating in a particular reaction have
melting temperatures that are within at least five degrees Celsius,
and more typically within two degrees Celsius of each other.
Primers are further designed to avoid priming on themselves or each
other. Primer concentration should be sufficient to bind to the
amount of target sequences that are amplified so as to provide an
accurate assessment of the quantity of amplified sequence. Those of
skill in the art will recognize that the amount of concentration of
primer will vary according to the binding affinity of the primers
as well as the quantity of sequence to be bound. Typical primer
concentrations will range from 0.01 .mu.M to 0.5 .mu.M.
[0135] In a typical PCR cycle, a sample including a DNA
polynucleotide and a PCR reaction cocktail is denatured by
treatment in thermal cycler at about 90-98.degree. C. for 10-90
seconds. The denatured polynucleotide is then hybridized to
oligonucleotide primers by treatment in a thermal cycler at a
temperature of about 30-65.degree. C. for 1-2 minutes. Chain
extension then occurs by the action of a DNA polymerase on the
polynucleotide annealed to the oligonucleotide primer. This
reaction occurs at a temperature of about 70-75.degree. C. for 30
seconds to 5 minutes. Any desired number of PCR cycles may be
carried out depending on variables including but not limited to the
amount of the initial DNA polynucleotide, the length of the desired
product and primer stringency. The above temperature ranges and the
other numbers are exemplary and not intended to be limiting. These
ranges are dependent on other factors such as the type of enzyme,
the type of container or plate, the type of biological sample, the
size of samples, etc. One of ordinary skill in the art will
recognize that the temperatures, time durations and cycle number
can readily be modified as necessary.
[0136] Several embodiments include quantitative real-time
polymerase chain reaction (qPCR), which is used to simultaneously
quantify and amplify a specific part of a given nucleic acid
molecule. It is used, for example, to determine whether or not a
specific sequence is present in the sample; and if it is present,
the number of copies in the sample.
[0137] qPCR monitors the fluorescence emitted during the reaction
as an indicator of amplicon production during each PCR cycle, as
opposed to endpoint detection. The real-time progress of the
reaction can be viewed in some systems. Typically, qPCR uses the
detection of a fluorescent reporter. Typically, the fluorescent
reporter's signal increases in direct proportion to the amount of
PCR product in a reaction. By recording the amount of fluorescence
emission at each cycle, it is possible to monitor the PCR reaction
during exponential phase where the first significant increase in
the amount of PCR product correlates to the initial amount of
target template. The higher the starting copy number of the nucleic
acid target, the sooner a significant increase in fluorescence is
observed. Thus, the procedure follows the general pattern of
polymerase chain reaction, but the nucleic acid molecule is
quantified after each round of amplification. In several
embodiments the amplified nucleic acid molecule is quantified by
the use of fluorescent dye that intercalates with double-strand
DNA. In other embodiments (e.g., when multiplex qPCR assays are
utilized) amplified nucleic acid molecule is quantified by use of
oligonucleotide probes labeled with a reporter fluorophore that can
be detected in the qPCR assay.
[0138] In certain embodiments, the amplified products are directly
visualized with detectable label such as a fluorescent DNA-binding
dye. In one embodiment the amplified products are quantified using
an intercalating dye, including but not limited to SYBR green, SYBR
blue, DAPI, propidium iodine, Hoeste, SYBR gold, ethidium bromide,
acridines, proflavine, acridine orange, acriflavine, fluorcoumanin,
ellipticine, daunomycin, chloroquine, distamycin D, chromomycin,
homidium, mithramycin, ruthenium polypyridyls, anthramycin. For
example, a DNA binding dye such as SYBR green binds double stranded
DNA and an increase in fluorescence intensity can be measured. For
example, the fluorescent dsDNA dye can be added to the buffer used
for a PCR reaction. The PCR assay can be performed in a thermal
cycler, and after each cycle, the levels of fluorescence are
measured with a detector, such as a camera. The dye fluoresces much
more strongly when bound to dsDNA (e.g., amplified PCR product).
Because the amount of the dye intercalated into the double-stranded
DNA molecules is typically proportional to the amount of the
amplified DNA products, the amount of amplified nucleic acid can be
quantified by detecting the fluorescence of the intercalated dye
using detection instruments known in the art. When referenced to a
standard dilution, the dsDNA concentration in the PCR can be
determined.
[0139] In addition to various kinds of fluorescent DNA-binding dye,
other luminescent labels such as sequence specific oligonucleotide
probes can be employed in the amplification reaction to facilitate
the detection and quantification of the amplified product. Probe
based quantitative amplification relies on the sequence-specific
detection of a desired amplified product. Unlike the dye-based
quantitative methods, it utilizes target-specific probe labeled
with a detectable marker such as a base-linked or terminally-linked
fluorophore and quencher. Such markers are known to the person of
ordinary skill in the art and described herein. Further, methods
for performing probe-based quantitative amplification are well
established in the art (see, e.g., U.S. Pat. No. 5,210,015).
[0140] For detection using oligonucleotide probes, the reaction is
prepared as usual for PCR conditions, with the addition of the
sequence specific labeled oligonucleotide probe. After denaturation
of the DNA, the labeled probe is able to bind to its complementary
sequence in the region of interest of the template DNA. When the
PCR reaction is heated to the proper extension temperature, the
polymerase is activated and DNA extension proceeds. As the
polymerization continues it reaches the labeled probe bound to the
complementary sequence of DNA. The polymerase breaks the probe into
separate nucleotides, and separates the fluorescent reporter from
the quencher. This results in an increase in fluorescence as
detected by the optical assembly. As PCR cycle number increases
more and more of the fluorescent reporter is liberated from its
quencher, resulting in a well-defined geometric increase in
fluorescence. This allows accurate determination of the final, and
initial, quantities of DNA.
[0141] In one embodiment, the fluorescently-labeled probes (such as
probes disclosed herein) rely upon fluorescence resonance energy
transfer (FRET), or in a change in the fluorescence emission
wavelength of a sample, as a method to detect hybridization of a
DNA probe to the amplified target nucleic acid in real-time. For
example, FRET that occurs between fluorogenic labels on different
probes (for example, using HybProbes) or between a donor
fluorophore and an acceptor or quencher fluorophore on the same
probe (for example, using a molecular beacon or a TAQMAN.TM. probe)
can identify a probe that specifically hybridizes to the DNA
sequence of interest. In some embodiments, the
fluorescently-labeled DNA probes used to identify amplification
products have spectrally distinct emission wavelengths, thus
allowing them to be distinguished within the same reaction tube,
for example in multiplex PCR, such as a multiplex qPCR.
[0142] Any type of thermal cycler apparatus can be used for the
amplification of, for example, HIV nucleic acids, as described
above and/or the determination of hybridization. Examples of
suitable apparatuses include PTC-100.RTM. Peltier Thermal Cycler
(MJ Research, Inc.; San Francisco, Calif.), a ROBOCYCLER.RTM. 40
Temperature Cycler (Agilent/Stratagene; Santa Clara, Calif.), or
GeneAmp.RTM. PCR System 9700 (Applied Biosystems; Foster City,
Calif.). For qPCR, any type of real-time thermocycler apparatus can
be used. For example, ICYCLER IQ.TM. or CFX96.TM. real-time
detection systems (Bio-Rad, Hercules, Calif.), LIGHTCYCLER.RTM.
systems (Roche, Mannheim, Germany), a 7700 Sequence Detector
(Perkin Elmer/Applied Biosystems; Foster City, Calif.), ABI.TM.
systems such as the 7000, 7300, 7500, 7700, 7900, or ViiA7 systems
(Applied Biosystems; Foster City, Calif.), or an MX4000.TM.,
MX3000.TM. or MX3005.TM. qPCR system (Agilent/Stratagene; Santa
Clara, Calif.), DNA ENGINE OPTICON.RTM. Continuous Fluorescence
Detection System (Bio-Rad, Hercules, Calif.), ROTOR-GENE.RTM. Q
real-time cycler (Qiagen, Valencia, Calif.), or SMARTCYCLER.RTM.
system (Cepheid, Sunnyvale, Calif.) can be used to amplify and
detect nucleic acid sequences in real-time. In some embodiments,
qPCR is performed using a TAQMAN.RTM. array format, for example, a
microfluidic card in which each well is pre-loaded with primers and
probes for a particular target. The reaction is initiated by adding
a sample including nucleic acids and assay reagents (such as a PCR
master mix) and running the reactions in a real-time thermocycler
apparatus.
III. Isolated Nucleic Acid Molecules and Compositions Comprising
Same
[0143] Isolated oligonucleotide primers (which as defined herein
also include the complementary sequence and corresponding RNA
sequences) for use in the disclosed methods, and compositions
comprising such primers, are provided herein.
[0144] The isolated oligonucleotide primers can comprise or consist
of at least 10 consecutive nucleotides (such as at least 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,
47, 48, 49, or 50 consecutive nucleotides) from a target nucleic
acid sequence (e.g., an HIV-1 sequence). For example, in some
embodiments, the isolated oligonucleotide primers can include or
consist of 10-50 nucleotides, such as, 12-15, 12-20, 12-25, 12-30,
12-35, 12-40, 12-45, 12-50, 14-15, 14-16, 14-18, 14-20, 14-25,
14-30, 15-16, 15-18, 15-20, 15-25, 15-30, 15-35, 15-40, 15-45,
15-50, 16-17, 16-18, 16-20, 16-22, 16-25, 16-30, 16-40, 16-50,
17-18, 17-20, 17-22, 17-25, 17-30, 18-19, 18-20, 18-22, 18-25,
18-30, 19-20, 19-22, 19-25, 19-30, 20-21, 20-22, 20-25, 20-30,
20-35, 20-40, 20-45, 20-50, 21-22, 21-25, 21-30, 22-25, 22-30,
22-40, 22-50, 23-24, 23-25, 23-30, 24-25, 24-30, 25-30, 25-35,
25-40, 25-45, or 25-50 consecutive nucleotides from a target
nucleic acid sequence.
[0145] In some embodiments, any of the probes or primers disclosed
herein can be of a maximum length, for example no more than 15, 25,
25, 40, 50, 75, 100, or 150 nucleotides in length. Any of the
isolated nucleic acid sequences disclosed herein may consist or
consist essentially of the disclosed sequences, or include nucleic
acid molecules that have a maximum length of 15, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75 or 80 contiguous nucleotides of the
disclosed sequence. The disclosed contiguous sequences may also be
joined at either end to other unrelated sequences.
[0146] In some embodiments, the oligonucleotide primers comprise or
consist of the sequence of any one of the primers listed herein,
such as a primer listed in Table 1 above. These oligonucleotides
can be employed as effective oligonucleotide primers for
amplification and/or detection of target nucleic acid molecule
sequences.
[0147] In some embodiments, the isolated nucleic acid molecule
comprises a plus primer comprising or consisting of the nucleic
acid sequence set forth as any one of SEQ ID NOs: 1-2, 4-5, 6-7,
9-12, 15-17, 19-20, or 39-42.
[0148] Compositions comprising one or more of the probes or primers
disclosed herein are also provided, and are useful, for example, in
the disclosed methods.
[0149] In some embodiments, the composition can include a primer
pair comprising a forward and a reverse primer for amplifying a
target nucleic acid molecule comprising a mutant first allele,
wherein the forward primer is a first plus primer comprising a
locked nucleic acid at the 3' end that is complementary to the
mutant first allele of the target nucleic acid molecule, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule. The composition can further include a first control
primer comprising a locked nucleic acid at the 3' end that is
complementary to a wildtype first allele corresponding to the
mutant first allele, and remaining nucleotides that are the same as
the first plus primer. In some such embodiments, the composition is
useful in methods for detecting a mutant allele of HIV-1 reverse
transcriptase, and the first plus primer, the first control primer,
and the reverse primer, comprise or consist of the nucleic acid
sequences set forth as one of: SEQ ID NOs: 1, 2, and 3,
respectively, SEQ ID NOs: 29, 41, and 3, respectively; SEQ ID NOs:
40, 42, and 3, respectively, SEQ ID NOs: 1, 2, and 37,
respectively, SEQ ID NOs: 29, 41, and 37, respectively, SEQ ID NOs:
40, 42, and 37, respectively, SEQ ID NOs: 1, 2, and 38,
respectively, SEQ ID NOs: 29, 41, and 38, respectively, SEQ ID NOs:
40, 42, and 38, respectively, SEQ ID NOs: 4, 5 and 3, respectively,
SEQ ID NOs: 4, 5, and 37, respectively, SEQ ID NOs: 4, 5, and 38,
respectively, SEQ ID NOs: 6, 7, and 8, respectively, SEQ ID NOs: 9,
10, and 10, respectively, SEQ ID NOs: 11, 12, and 14, respectively,
SEQ ID NOs: 15, 12, and 14, respectively, SEQ ID NOs: 16, 17, and
17, respectively, or SEQ ID NOs: 19, 20, and 20, respectively.
[0150] In some embodiments, the composition can include a primer
pair comprising a forward and a reverse primer for amplifying a
target nucleic acid molecule comprising a mutant first allele and a
mutant second allele, wherein the forward primer is a first plus
primer comprising a locked nucleic acid at the 3' end that is
complementary to the mutant first allele of the target nucleic acid
molecule, a mismatch nucleotide at the -1 position from the 3' end
that is not complementary to the target nucleic acid molecule, and
remaining nucleotides that are complementary to the target nucleic
acid molecule, and the reverse primer of the test primer pair is a
second plus primer comprising a locked nucleic acid at the 3' end
that is complementary to the mutant second allele, a mismatch
nucleotide at the -1 position from the 3' end that is not
complementary to the target nucleic acid molecule, and remaining
nucleotides that are complementary to the target nucleic acid
molecule. The composition can further include a first control
primer comprising a locked nucleic acid at the 3' end that is
complementary to a wildtype first allele corresponding to the
mutant first allele, and remaining nucleotides that are the same as
the first plus primer, and a second control primer comprising a
locked nucleic acid at the 3' end that is complementary to a
wildtype second allele corresponding to the mutant second allele,
and remaining nucleotides that are the same as the second plus
primer. In some such embodiments, the composition is useful in
methods for detecting first and second mutant alleles of HIV-1
reverse transcriptase, and the first plus primer, the first control
primer, the second plus primer, and the second control primer,
comprise or consist of the nucleic acid sequences set forth as SEQ
ID NOs: 1, 2, 6, and 7, respectively, or SEQ ID NOs: 1, 2, 9, and
10, respectively.
[0151] The isolated nucleic acid molecules and/or compositions
disclosed herein can be supplied in the form of a kit for use in an
assay to identify or characterize a target nucleic acid molecule.
In such a kit, an appropriate amount of one or more of the primers
disclosed herein, are provided in one or more containers. A nucleic
acid probe may be provided suspended in an aqueous solution or as a
freeze-dried or lyophilized powder, for instance. The container(s)
in which the nucleic acid(s) are supplied can be any conventional
container that is capable of holding the supplied form, for
instance, microfuge tubes, ampoules, or bottles. Control reagents,
such as control nucleic acid molecules can also be included.
[0152] In some examples, one or more sets of primers, may be
provided in pre-measured single use amounts in individual,
typically disposable, tubes or equivalent containers. With such an
arrangement, the sample to be tested for the presence of the target
nucleic acids can be added to the individual tube(s) and
amplification carried out directly.
[0153] The amount of nucleic acid probe supplied in the kit can be
any appropriate amount, and may depend on the target market to
which the product is directed. For instance, if the kit is adapted
for research or clinical use, the amount of each nucleic acid
primer provided would likely be an amount sufficient to prime
several detection reactions.
[0154] In some embodiments, kits also may include the reagents
necessary to carry out ASPCR assays, including sample preparation
reagents, appropriate buffers, salts, tubes or assay cells. In
other particular embodiments, the kit includes equipment, reagents,
and instructions for extracting and/or purifying nucleic acid
molecules from a sample.
EXAMPLE
[0155] The following example is provided to illustrate particular
features of certain embodiments, but the scope of the claims should
not be limited to those features exemplified.
Example 1
Allele Specific PCR Assay for the Detection of HIV-1 Minor Variants
and Linked Drug Resistance Mutations
[0156] This example illustrates a novel Allele-Specific PCR (ASPCR)
assay that provides improved specificity and sensitivity compared
to known assays for detecting variations in a target nucleic acid
sequence. Standard ASPCR serves as a good alternative to standard
genotypic and phenotypic HIV-Drug Resistance (HIVDR) assays,
addressing limitations associated with these assays, such as low
sensitivity and high cost. Even though ASPCR is used in research
settings, routine use in the clinic has been precluded due to
issues associated with: demand of high stringency conditions,
vulnerability to HIV polymorphism, PCR artifacts, and detection of
one mutation at a time. This example describes an improved ASPCR
assay that addresses the above issues. Using primers that carry
both a penultimate mismatch and a 3' Locked Nucleic Acid (LNA), the
discriminatory power of ASPCR between mutant and wild type
templates was increased. Additionally, by introducing a new method
for normalization, which is based on the delta Ct (.DELTA.Ct)
between the allelic specific reaction and a reaction that uses
degenerative primers at the 3' end for the studied mutation, issues
with HIV polymorphism were addressed. These modifications generated
a more robust assay. In addition, by replacing the use of Taq
polymerase during the first round amplification with a 3.sup.rd
generation proof reading polymerase, the background of the assay
was reduced, and associated PCR artifacts were eliminated. Finally,
using an allele specific primer for both the forward and the
reverse primer, it was possible to detect two mutations in one
reaction, and determine their linkage. The improved ASPCR assay can
serve as a simplified method for surveillance and monitoring of HIV
drug resistance.
INTRODUCTION
[0157] In several clinical studies, HIV drug-resistance (HIVDR)
testing has been associated with better patient management,
improved virological and clinical outcomes, and better overall
survival (Palella et al., Ann. Intern. Med. 151:73-84, 2009; Cortez
et al., Viruses 3:347-378. doi:10.3390/v3040347, 2011). HIVDR
testing is recommended for selection and optimization of
antiretroviral (ARV) therapy in patient management, as summarized
in the DHHS Antiretroviral Guidelines for the Treatment of Adult
and Adolescents HIV infections (Guidelines for the Use of
Antiretroviral Agents in HIV-1-Infected Adults and Adolescents.
2013. (aidsinfo.nih.gov/guidelines)). HIV drug resistance assays
are either phenotypic or genotypic based. Phenotypic assays use the
generation of recombinant viruses that subsequently are tested for
growth in Drug Susceptibility Assays against varying drug
concentrations (Hertogs et al., Antimicrob. Agents Chemother.
42:269-276, 1998; Petropoulos et al., Antimicrob. Agents Chemother
44:920-928, 2000). Genotypic assays involve sequencing or base
point detection of known mutations that confer drug resistance.
There are two commercially and FDA-approved HIV-1 genotyping tests,
the TruGene genotyping assay (Grant et al., J. Clin. Microbiol.
41:1586-1593, 2003) and the ViroSeq HIV-1 genotyping system
(Eshleman et al., J. Clin. Microbiol. 43:813-817, 2005), and
several "in house" assays, that are performed by reference
laboratories for HIVDR and surveillance.
[0158] A major limitation of standard HIV drug resistance assays is
the lack of sensitivity to detect low-frequency drug-resistance
variants that are present at a frequency of less than 20% (Church
et al., J. Mol. Diag. 8:430-432, 2006; Tsiatis et al., J. Mol.
Diagn. 12:425-432, 2010). As per DHHS guidelines, HIVDR testing is
recommended to be performed while patient is under ARV therapy or
during a short period after treatment interruption, as without the
drug-selection pressure the wild-type virus quickly becomes the
dominant population, dropping resistant variants below the
detection limit (Guidelines for the Use of Antiretroviral Agents in
HIV-1-Infected Adults and Adolescents. 2013.
(aidsinfo.nih.gov/guidelines)). Failure to detect these minority
resistant variants can result in poor clinical treatment outcomes.
The importance of these minority variants has been best
demonstrated in women that received single dose nevirapine, where
the presence of low frequency mutations was associated with
subsequent nevirapine containing regimen failure (Jourdain et al.,
N. Engl. J. Med. 351:229-240, 2004; Boltz et al., PNAS.
22:9202-9207, 2011).
[0159] For the detection of these minority variants, several assays
with increased sensitivity have been developed, but have not
entered routine clinical testing. Single Genome Sequencing (SGS)
and Ultra-Deep Pyrosequencing (UDPS) offer an advantage over
genotyping or detecting minor variants; however, their high cost,
the need for IT support as in the case for UDPS or the high labor
demands of SGS, have limited their routine use (Palmer et al., J.
Clin. Microbiol. 43:406-413, 2005; Margulies et al., Nature.
15:376-380, 2005; Wang et al., Genome Res. 17:1195-1201, 2007).
Several other methods have been developed with lower cost including
oligoligase assay (OLA), LigAMP, allele-specific or
mutation-specific real time PCR (ASPCR), and parallel
allele-specific sequencing (PASS) (Villahermosa et al., J Clin
Microbiol. 4:238-248, 2001; Shi et al., Nat. Methods. 1: 141-147,
2004; Little et al., Curr. Protoc. Hum. Genet. 2001. Chapter 9:
Unit 9.8. doi:10.1002/0471142905.hg0908s07, 2001; Palmer et al.,
PNAS 103:7094-7099, 2006; Cai et al., Nat. Methods. 4: 123-125,
2007).
[0160] ASPCR is the most common method used for the detection of
minority variants, characterized by increased sensitivity and low
cost, but its use is limited to the research setting. According to
Johnson et al., the main reasons that ASPCR has not entered into
clinical practice is attributed to; i) the stringent conditions
that are required to ensure accuracy, ii) the ability to target
only one mutation at a time, iii) the absence of detecting linkage,
iv) PCR artifacts that can result in false positives, and v) the
presence of polymorphisms throughout the HIV genome that can affect
primer binding and require the use of subtype-specific primers
(Johnson et al., J. Antimicrob. Chemother. 65:1322-1326). A number
of assays have been developed to address these issues, specifically
those associated with sensitivity and linkage. One of these assays
combines the sensitivity of ASPCR with mutation-specific amplicon
sequencing, allowing detection of linked drug resistance mutations
(Johnson et al., PLoS One 2: e638, 2007.
doi:10.1371/journal.pone.0000638), and recently a multiplex
allele-specific (MAS) assay utilizing 45 allele-specific reactions
using primers tagged with oligonucleotide multiplex identifiers
that can bind to microspheres that are analyzed with a suspension
array system (Zhang et al., J. Clin. Microbiol. 51:3666-3674,
2013).
[0161] This example describes a novel ASPCR assay that provides
increase sensitivity and specificity compared to prior assays. The
new assay addresses the above issues, which could potentially allow
ASPCR to enter the clinic either alone or in combination with a
multiplexing technology, as a sensitive HIV-DR assay for patient
care, surveillance, and monitoring. Furthermore the new assay
expands applications of ASPCR to address linked drug resistance
mutations that are important for combination antiretroviral therapy
(cART) and could allow for the development of therapy tailored
sensitive diagnostic assays.
Materials and Methods
[0162] Viruses and Viral Mixtures.
[0163] Viral stocks with wild-type 184V (AGT) or mutant 184V (GTG)
were generated by CaPO4 transfections into 293T cells using
infectious plasmid clones of HW-1.sub.LAI. Defined virus mixtures
at varying ratios (0, 0.01, 0.1, 0.4, 1, 2, 5, 10, 25, 50, and 100%
mutant) were prepared in HIV-seronegative human plasma using the
viral stocks. Viral mixtures were generated to a final average copy
number of 2.6.times.10.sup.5 copies/ml as determined by Amplicor
HIV-1 Monitor Assay (Roche; Indianapolis, Ind.), stored at
-80.degree. C., and tested as a blinded panel.
[0164] Clinical Specimens.
[0165] All participants provided written informed consent and
testing was approved by Institutional Review Board of the
University of Pittsburgh.
[0166] Generation of HIV-1 subtype C standards.
[0167] Standards were generated from a cloned pro/pol subtype C 2.2
kb fragment (GenBank accession no AF286227) into pTriAmp plasmid
from the HIV-1 strain 97ZA012 from South Africa. To this plasmid
the K65R (AAG.fwdarw.AGG), K70E (AAG.fwdarw.GAG), M184V
(ATG.fwdarw.GTG), M184I (ATG.fwdarw.ATA), or the double K65R/M184V
mutations were introduced using the QuickChange II XL Site-Directed
Mutagenesis kit (Statagene; La Jolla, Calif.). From these plasmids
a 636 bp DNA fragment was amplified using the Phusion Hot Start II
High Fidelity kit (Thermo Scientific; Waltham, Mass.) and gel
purified using a DNA isolation kit (Qiagen; Venlo, Limburg,
Holland). For comparative purposes, Phusion was substituted by
AmpliTaq Gold (Life Technologies; Carlsbad, Calif.).
[0168] RNA Extraction and First Round Amplification.
[0169] Virus was pelleted from 500 .mu.l of plasma by
centrifugation at 24,000.times.g for 1 hr at 4.degree. C.
Supernatants were removed, the pellets were resuspended in 100
.mu.l of 3M GuHCl (Fisher Scientific: Waltham, Mass.) with
Proteinase K (100 .mu.g/ml) (Ambion: Grand Island, N.Y.), and
incubated at 42.degree. C. for 1 hr to digest the virions.
Subsequently 400 .mu.l of 6M GuSCN (Sigma-Aldrich; St. Louis. Mo.)
containing 200 .mu.g of glycogen were added, and viral RNA was
pelleted with 500 .mu.l of isopropanol following centrifugation at
21,000.times.g for 15 min. The pellet was washed with 70% EtOH,
dried, and resuspended in 30 .mu.l of 5 mM Tris pH 7.8, containing
1 mM DTT (Fisher Scientific; Waltham, Mass.), and 1 U/.mu.l of
RNasin (Fisher Scientific; Waltham, Mass.). First round
amplification from cDNA was performed utilizing subtype C specific
primers, 5'-AAACAATGGCCATTGACAGAAGA-3' forward (SEQ ID NO: 21), and
5'-GTTCATACCCCATCCAAAGAAATG-3' reverse (SEQ ID NO: 22). For the
PCR, either AmpliTaq Gold (Life Technologies) or Phusion Hot Start
II High Fidelity (Thermo Scientific) was used and for comparison
reasons. In order to quantify the number of cDNA copies that the
amplified PCR derived from, we run a real time PCR reaction using
SYBR green that compared to dsDNA standards that multiplied by 2 to
calculate ssDNA copies. The amplification conditions using Phusion
were 98.degree. C. for 10 seconds, 49.degree. C. for 20 seconds,
and 72.degree. C. for 40 seconds for a total of 40 cycles.
[0170] Primers for Allele Specific PCR.
[0171] The ASPCR primers for the detection of K65R in subtype C
HIV-1 virus are; K65R forward 5'-CTCCARTATTTGCCATAAAACG-3' (SEQ ID
NO: 23, PEN), 5'-CTCCARTATTTGCCATAAAAA+G-3' (SEQ ID NO: 24, LNA) or
5'-CTCCARTATTTGCCATAAAAC+G-3' (SEQ ID NO: 1, PLUS), K65WT forward
5'-CTCCARTATTTGCCATAAAACA-3' (SEQ ID NO: 25, PEN),
5'-CTCCARTATTTGCCATAAAAA+A-3' (SEQ ID NO: 26, LNA) or
5'-CTCCARTATTTGCCATAAAAC+A-3' (SEQ ID NO: 2, PLUS), and a common
reverse primer K65REV 5'-TATTCCTAATTGAACYTCCCA-3' (SEQ ID NO: 3).
For calculation of total copies the K65total
5'-CTCCARTATTTGCCATAAAAA-3' (SEQ ID NO: 35) was used.
[0172] For the detection of M184V the following primers were used;
M184V reverse 5'-CTAAGTCAGATCCTACATACAAGTCATCCCC-3' (SEQ ID NO: 27,
PEN) or 5'-CTAAGTCAGATCCTACATACAAGTCATCCC+C-3' (SEQ ID NO: 6,
PLUS), M184V/WT reverse 5'-CTAAGTCAGATCCTACATACAAGTCATCCCT-3' (SEQ
ID NO: 28, PEN) or 5'-CTAAGTCAGATCCTACATACAAGTCATCCC+T-3' (SEQ ID
NO: 7, PLUS), and a common forward primer M184FW common primer
5'-TAGTATAAACAATGAGACACCAGGGATTA-3' (SEQ ID NO: 8). For the
detection of M184I the following primers were used; M184I reverse
5'-CCCTATTTCTAAGTCAGATCCTACATACAAGTCATGT-3' (SEQ ID NO: 29, PEN) or
5'-CCCTATTTCTAAGTCAGATCCTACATACAAGTCATG+T-3' (SEQ ID NO: 9, PLUS),
M184I/WT reverse 5'-CCCTATTTCTAAGTCAGATCCTACATACAAGTCATGC-3' (SEQ
ID NO: 30, PEN) or 5'-CCCTATTTCTAAGTCAGATCCTACATACAAGTCATG+C-3'
(SEQ ID NO: 10, PLUS), and the M184FW (SEQ ID NO: 8) as a common
forward primer. For calculation of total copies for both M184V and
M184I, the M184 total primer
5'-CTATTTCTAAGTCAGATCCTACATACAAGTCATC-3' (SEQ ID NO: 31) was
used.
[0173] Primers containing locked nucleic acids were ordered from
Exiqon (Woburn, Mass.). All primers were PAGE purified to avoid
mispriming and false amplifications, and used at 300 nM
concentration for the allele specific PCR reactions.
[0174] Allele Specific PCR.
[0175] Amplified virus template from first round amplification of
clinical samples or standards was diluted down to 10.sup.6
copies/.mu.l and 5.times.10.sup.6 copies were analyzed by ASPCR for
the detection of the specific allele of interest. Each sample was
run in 25 .mu.l reactions in triplicate using SYBR Green Core
Reagents (Life Technologies; Carlsbad, Calif.) containing 2.5 .mu.l
of 10.lamda. SYBR Green, 1 .mu.l of 12.5 mM dNTPs with UTP, 3.5
.mu.l of 25 mM MgCl.sub.2, 0.75 .mu.l of Upper Primer, 0.75 .mu.l
of Lower Primer, 0.25 .mu.l of 5 U/.mu.l AmpliTaq Gold (Applied
Biosystems; Foster City, Calif.), and 5 .mu.l of first round
template (10.sup.6 copies/O. qPCR was performed in either a ViiA7
(Applied Biosystems; Foster City, Calif.) or CFX-96 (BioRad;
Hercules, Calif.) real-time thermal cycler. The amplification
conditions were, 95.degree. C. for 12 min hot-start incubation,
95.degree. C. for 15 seconds, 55.degree. C. for 20 seconds, and
69.degree. C. for 1 minute for a total of 50 cycles.
[0176] Data Analysis.
[0177] Standard curves, based on the .DELTA.Cts between the allele
specific reaction and the total or mixed primer reaction, were
generated for half log serial dilutions of mutants in wild-type
background from 100% mutant down to 0.001%. Fitting was performed
using XLfit, a fitting software for Excel (IDBS). Percent mutant
present in samples was calculates based on their .DELTA.Ct and the
corresponding fitted standard curve.
Results
[0178] Increased Discriminatory Power with PLUS Primers for
ASPCR.
[0179] Three primer designs were tested for the development of an
ASPCR assay for the detection of the K65R mutation in subtype C
HIV-1 virus. The first includes the introduction of a locked
nucleic acid (LNA) at the 3' position of the allele specific
primer, while the second introduces a mismatch at the penultimate
site (PEN), the -1 position from the 3' end. These designs were
compared to a third, including both modifications in one AS primer
designated as PLUS, for their ability to discriminate between wild
type and mutant templates by ASPCR. FIG. 1 shows the differences in
amplification efficiencies, expressed as a .DELTA.Ct between the
65R and the 65K template. ASPCR was performed at two different
annealing temperatures of 55.degree. C. and 61.degree. C.,
respectively. Under both conditions the PLUS primer exhibited an
increased .DELTA.Ct by 2 cycles when compared to the PEN primer
(.DELTA.Ct of 8.9 vs. 7.2 at 55.degree. C. and .DELTA.Ct of 10.9 vs
8.9 at 61.degree. C.). In contrast, the LNA primer was less
efficient than both the PLUS and PEN primers, regardless of
conditions used (55.degree. C. vs. 61.degree. C.). In order to
confirm that the increased discriminatory power of the PLUS primer
design can increase the discriminatory power of the ASPCR, and was
not unique for the K65R assay, both PLUS and PEN allele specific
primers of identical sequence were also synthesized for the M184V
and M184I mutant alleles of HIV-1 reverse transcriptase gene. Both
primer designs were tested at gradient annealing temperatures
ranging from 55.degree. C.-65.degree. C. against the wild type and
the mutant 184V or the 184I templates. As depicted, the PLUS primer
design increased the .DELTA.Ct of the ASPCR for M184V (FIG. 2A) by
3 cycles (16 vs. 13) at 65.degree. C. and by 5 cycles (16 vs. 11)
at 55.degree. C. when compared to the corresponding PEN design. The
improvement in discrimination was also observed for the M184I
template. This was characterized by an increase of the .DELTA.Ct by
3 cycles (16 vs. 13) (FIG. 2B) across all temperatures tested in
the gradient, confirming the increased discriminatory power of the
PLUS design.
[0180] New Method for ASPCR Normalization.
[0181] Due to the highly polymorphic nature of HIV, ASPCR is
vulnerable to inaccurately estimating the concentration of an
allele present and is prone to false positive as well as false
negative results. Under current ASPCR methodologies, the allele
specific PCR reactions against mutant or wild type virus template
are normalized with a third qPCR reaction that estimates the total
copy number (FIG. 3A). However, this total reaction can also be
affected by HIV polymorphisms, displaying large differences on the
amplification efficiencies observed with clinical samples.
Alternatively, total copies can be calculated with a qPCR reaction
in the same position as the allele specific reaction by moving the
total primer upstream by one or two bases (FIG. 3A). Despite this
approach, polymorphisms in proximity to the 3' end of the allele
specific primer (FIG. 3B), can still exert large effects on
amplification efficiencies between allelic specific and total
reaction, producing erroneous results. As illustrated in FIGS. 3C
and 9, a new method for normalization was developed and tested,
where the allele specific reaction was normalized against a PCR
reaction that utilizes both the mutant and the wild type AS primers
in one three primer or five primer PCR reaction (degenerative
primer at the 3' end position). The new method was tested using 10
clinical samples positive for subtype C HIV-1 virus and with
available standard genotyping data (FIG. 6). Four of these samples
were positive for the M184V mutation present at frequencies of
50-100% as determined by standard genotyping (ViroSeq; Celera). One
of ten samples was positive for K65R mutation at a frequency of 20%
and the remaining five samples were negative for the presence of
the mutations at these two sites. ASPCR was performed using the
PLUS primers and normalized with either the old or the new method.
Normalization with the old method produced erroneous results for
samples 9 and 10 characterized by the presence of M184V at a
frequency greater than 100% (1,168 and 124%). Utilizing the new
method of normalization, the frequency of M184V in samples 9 and 10
was calculated to be 51% and 44%, respectively. These values are in
agreement with the estimated values based on their corresponding
electropherograms, showing a clear improvement over the old method.
Conversely, the presence of K65R in sample 1 was not detected by
either the old or new method, despite its presence at a frequency
of 20% by standard genotyping.
[0182] Further, as the new method is based on the Delta Ct it can
compensate for differences between primers and template, for
example in the case of different HIV-1 subtypes with varying
polymorphisms. FIG. 9 illustrates an example of testing for K65R
mutation in samples with subtype C HIV. Even though a sample with
Type A virus has a G at -2 position adjacent to the penultimate
mismatch, and amplification is delayed by 10 cycles, results are
still translatable. In this example a Delta Ct of 8 is below the
0.1% cutoff of the assay or a Delta Ct of 7 (Range -3 to 7).
[0183] Reduction of Background and Limit of Detection with Proof
Reading Polymerase.
[0184] The absence of K65R in sample 1 was suggestive of a false
positive, attributed to the utilization of a non-proof reading
polymerase during first round amplification. In order to compensate
for the possible introduction of errors during PCR, a proof reading
polymerase during this initial amplification was used. The 10
clinical samples were retested by ASPCR for the presence of M184V
and K65R using Phusion, a proof reading polymerase with a 3' to 5'
exonuclease activity. A comparison between a non-proof reading
(Taq) and a proof reading polymerase (Phusion) is illustrated in
FIG. 4. The results obtained for the four positive M184V samples
were concordant, between Taq and Phusion (Sample #7, 71.3% vs.
79.4%; Sample #8, 92.2% vs. 71.8%; Sample #9, 51.4% vs. 62.4%; and
Sample 10, 43.6% vs. 48.0%), respectively. Furthermore, for samples
negative for M184V as determined by standard genotyping, background
levels decreased by 1 log (0.1% to values below 0.01%). More
impressive were the results obtained for K65R, where a more than 2
log reduction was observed from 1% to below 0.01%, the limit of
detection for this assay based on standards amplified from
plasmids. As observed previously, Sample 1 was shown to be negative
for K65R.
[0185] Validation Using Viral Mixtures.
[0186] The new ASPCR assay with the new primer design, new method
of normalization, and the use of a proof-reading polymerase during
the first round of amplification was validated using a blinded
panel of 184V/wild-type viral mixtures spiked into negative human
plasma at an average of 2.6.times.10.sup.5 copies/ml (FIG. 7). The
values for 184V allele, as detected by ASPCR, were in accordance
with expected values. A linear regression analysis of the input
percent value of the mixtures versus the average calculated by
ASPCR revealed a slope of 0.82 with an R.sup.2 of 0.99. The CV for
the negative sample was 36% and below 33% for all the positive
samples. The limit of detection was down to 0.1%.
[0187] Detection of Linked Mutations Using ASPCR.
[0188] One limitation of current ASPCR technology is the detection
of only one mutation at a time, limiting its application in the
detection of linked drug-resistance mutations. However, the
question of linkage can be addressed by the exploitation of our new
methodology and the degenerative primer design (FIG. 3C), by
utilizing allele specific primers for both the forward and reverse
oligonucleotides used during 2.sup.nd round PCR. This allows for
the detection of two mutations at time and addresses the question
of linkage. To test the concept of detecting linked mutations using
ASPCR, standards were generated that harbored both the K65R and the
M184V drug-resistance mutations. For the detection of these linked
mutations the forward allele specific primer for K65R and the
reverse allele specific primer for M184V were used, and tested in a
qPCR reaction for their ability to discriminate between four
standard templates; K65R/M184V (double mutant), K65R (single
mutant), M184V (single mutant), or wild type (no mutant). As shown
in FIG. 5A the double allele specific ASPCR had the ability to
discriminate with a .DELTA.Ct of 11 cycles over the M184V template,
a .DELTA.Ct of 16 cycles over the K65R template, and a .DELTA.Ct of
19 cycles over the wild type template. Using the new ASPCR method
as depicted in FIG. 5B, and serial dilutions of standards of the
double mutant in backgrounds of wild type, K65R, M184V, or mixtures
of the three, showed a consistent detection limit below 0.1%, for
all the different backgrounds used.
[0189] The assay was further validated using six clinical samples
from patients that had failed first line therapy. Standard
genotyping data were available for these six samples showing
presence of K65R, M184V or both (FIG. 7). Quantification of linked
K65R and M184V mutations was based on two standard curves, one with
serial dilution of the double mutant in K65R background and one
with serial dilutions of the double mutant in the M184V background.
Linkage was detected in 5 out of the 6 samples, otherwise missed by
standard genotyping (5 of 6 vs. 2 of 6). Calculated values of
percent linked mutations were in concordance for both standard
curves with either a K65R or M184V background.
DISCUSSION
[0190] This example illustrates the development of an improved
method for performing ASPCR for the detection of HIV-1 variants,
including minor variants. The new method addresses issues
associated with current ASPCR methods whose application in the
clinical setting is limited. Improvements in current methodology
includes the utilization of, a) a new primer design to increase
sensitivity, b) a new method of normalization that minimizes
variability associated with HIV polymorphism, c) employment of a
proof reading polymerase to minimize false positives and a reduce
background, and finally d) the ability to detect linkage between
two drug resistance mutations, which is more relevant in a clinical
setting than the detection of a single point mutation.
[0191] Currently, two primer designs have been recommended for
their use in ASPCR to increase the discriminatory power of the
assay between mutant and wild type templates. The first, described
in the amplification refractory mutation system (ARMS), includes
the introduction of a mismatch at the penultimate site (PEN),
improving the assay for certain mismatch combinations that are
poorly discriminated (Little et al., Curr. Protoc. Hum. Genet.
2001. Chapter 9: Unit 9.8. doi:10.1002/0471142905.hg0908s07, 2001).
The second design incorporates a locked nucleic acid (LNA), a
nucleic acid analog with a 2'-O, 4'-C methylene bridge at the 3'
end of the allele specific primer, which increases discrimination
for all mismatch combinations (Latorra et al., Hum. Mutat.
22:79-85, 2003).
[0192] In an attempt to develop an ASPCR assay for the detection of
the K65R mutation in subtype C HIV-1 virus, three different primer
designs with identical sequences were compared which included LNA,
PEN, and PLUS primers, the later a combination of the LNA and PEN
primers, respectively (FIG. 1). The novel PLUS design improved the
discriminatory power of the assay between the 65R and the 65K wild
type templates characterized by a .DELTA.Ct increase of at least of
2 and 4 cycles when compared to PEN and LNA designs, respectively.
Furthermore, despite these combined modifications, qPCR was only
moderately compromised (PLUS Ct of 18 vs. Ct of 16 for PEN and
LNA). This increased mismatch discrimination property associated
with the PLUS primers was not unique for the K65R but also
confirmed for the M814V and M184I ASPCR assay, suggesting that this
is a generalized property. Surprisingly, for the M184V ASPCR, the
.DELTA.Ct was more stable across a temperature gradient when
comparing PLUS to PEN primers, suggesting that the increase in
discrimination is not only due to an increase in Tm with the
introduction of the LNA, but a restriction in the conformation of
the 3' end of primer may also play a role (Nielsen et al., J Biomol
Struct Dyn 17:175-190, 1999).
[0193] Testing the prior ASPCR assay using with clinical samples
revealed some erroneous results as shown in FIG. 6. One of the main
hurdles for ASPCR is that the HIV genome is highly polymorphic and
PCR efficiencies are altered from sample to sample depending on the
number of mismatches that exists between the AS primer and the
template. In order to compensate for this, the values from the
original allele specific PCR reaction are normalized against a
reaction that amplifies the total copies. Still, this total
reaction is vulnerable to polymorphism, making very difficult to
normalize the data accurately. Alternatively, utilization of
primers that are at the same site as the allele specific primer
missing the 3' mismatch, even though is a good approximation, still
can be affected by polymorphism. However, both approaches can
succumb to the impact of polymorphisms as observed in FIG. 3B (i.e.
-3 vs. -2 positions). To compensate for these discrepancies,
investigators can introduce criteria to eliminate erroneous results
(Boltz et al., PNAS. 22:9202-9207, 2011), or in cases that
genotypic data is available, use patient-specific HIV consensus
sequences for primer design (Rowley et al., J. Virol. Methods.
149:69-75, 2008; Boltz et al., J. Virol. Methods. 164:122-126,
2010).
[0194] In the new ASPCR method described in this example, the data
are normalized against a total reaction that uses a degenerative
primer at the 3' end of the allele-specific primer and the same
exact paired reverse or forward primer as in the ASPCR reaction.
The advantage of the new method is several-fold. First, differences
in the amplification efficiencies between the total and the
allele-specific PCR can result only from the 3' mismatch. Second,
the new method is also more simplified, as for each sample two
reactions are run in parallel to calculate the .DELTA.Ct of the
total vs. the allele specific reaction. Third, the concentration of
mutant is calculated based on the .DELTA.Ct of standards of known
mixtures. Therefore, competition that exists in the total reaction
is incorporated in the standards starting with a .DELTA.Ct of -1
for 100% mutant, with the allele specific reaction to be more
efficient, to a .DELTA.Ct up to +15 for 100% wild type, depending
the discriminatory power of the assay. As shown in FIG. 6, when we
compared the new to the old method, observed vs. expected results
were more concordant.
[0195] Validation of the K65R ASPCR assay using clinical samples
showed that a sample that was positive for K65R by standard
genotyping (AA/GG) was not detected and the negative result was
confirmed by repeated testing either by additional ASPCR or
standard genotyping. Utilization of a non-proof reading enzyme
during first round amplification such as Taq, can result in such
artifacts. Taq, with an error rate of 10.sup.-4 errors/base, lacks
3'-5' exonuclease activity and is prone to of nucleotides,
specifically A,T.fwdarw.G,C transitions, as is the case for K65R
(AAG.fwdarw.AGG) (Tindall et al., Biochemistry. 27: 6008-6013,
1988). In addition, this effect can be compounded in samples with
low viral loads where a misincorporation in the initial rounds of
amplification can have a "jackpot effect" resulting in false
positive results. Vargese et al. have reported similar results for
spurious detection of K65R in PCR-dependent sequencing (Varghese et
al., PLoS ONE 5(6):e10992. Doi:10.1371/journal.pone.0010992, 2010).
These findings suggest that misincorporations during 1.sup.st round
PCR can prove to be a major issue, due to the increased sensitivity
associated with ASPCR. Replacing Taq with Phusion, a proof-reading
polymerase with a 3' to 5' exonuclease activity, was shown to have
a large impact by a) eliminating false positives, b) reducing
background, and c) increasing the sensitivity of the assay. This is
evident in the case of K65R where the background of the assay with
clinical samples was reduced by two logs from 1% down to 0.01%,
values that were achieved before only with standards from plasmids,
where proof reading is present.
[0196] Finally, using the new methodology for ASPCR the linkage of
resistance mutations was addressed. The fact that the exact same
amplicon was utilized as an internal control for normalization,
provided the opportunity to include allelic specific primers for
both the forward and the reverse primer, as shown in FIG. 5, and
allowed for samples to be normalized with a PCR reaction using
forward and reverse degenerative primers. The new assay was tested
for the detection of K65R and M184V, mutations that are associated
with resistance to TRUVADA (combination therapy of tenofovir (65R)
and FTC (184V) (Masho et al., Ther. Clin. Risk Manag. 3:1097-1104,
2007). A template that has both resistance mutations was
differentially amplified from the wild type template or the
templates carrying either the individual K65R or M184V mutations
separately. Discrimination for the M184V template was determined to
be at a .DELTA.Ct of 11 cylces (the discriminatory power of the
K65R allele specific primer), and for the K65R template a .DELTA.Ct
of 16 (the discriminatory power of the M184V allele specific
primer). Due to differences in discriminatory power between
primers, the primer with the lower discriminatory power was set as
the lower limit of sensitivity of the linked assay, which in this
case was the K65R primer (0.1%). Furthermore, discrimination
increases if the standards were run in a mixed background with any
combination of K65R, M184V, or wild-type templates as well as all
three templates together, while the .DELTA.Ct at the certain
concentrations of standards remains the same. Applying the assay to
test clinical samples from patients that had failed first line
therapy revealed the presence of linked mutations in five out of
six tested, while standard genotyping detected linkage in only in
two of six. The absence of detection of linkage by standard
genotyping in these three of six samples could be attributed to
fitness of the virus. Previous reports have shown that the presence
of both K65R and M184V mutations render the virus less fit which
makes it difficult to maintain levels that can be detected with
standard genotyping, in the absence of drug pressure (Deval et al.,
J. Biol. Chem. 279:509-516, 2004). Truvada is the most common
prescribed combination drug for HIV that has also been recently
approved for prophylaxis and detection of linked resistance to
tenofovir and FTC at the sensitivity and cost that ASPCR offers
could be very important.
[0197] In conclusion, this example describes an improved and
simplified method for performing ASPCR with the potential to enter
the clinic as a new diagnostic test for drug resistance either
alone or in combination with a multiplexing technology. In
addition, the methodology has the added advantage in that it can
detect linked mutations, allowing for development of sensitive
diagnostic resistance assays, tailored to specific therapies.
[0198] It will be apparent that the precise details of the methods
or compositions described may be varied or modified without
departing from the spirit of the described embodiments. We claim
all such modifications and variations that fall within the scope
and spirit of the claims below.
Sequence CWU 1
1
48122DNAArtificial sequenceoligonucleotide primer 1ctccartatt
tgccataaaa cg 22222DNAArtificial sequenceoligonucleotide primer
2ctccartatt tgccataaaa ca 22321DNAArtificial
sequenceoligonucleotide primer 3tattcctaat tgaacytccc a
21425DNAArtificial sequenceoligonucleotide primer 4gccataaaaa
agaaggacca gtacg 25525DNAArtificial sequenceoligonucleotide primer
5gccataaaaa agaaggacca gtaca 25631DNAArtificial
sequenceoligonucleotide primer 6ctaagtcaga tcctacatac aagtcatccc c
31731DNAArtificial sequenceoligonucleotide primer 7ctaagtcaga
tcctacatac aagtcatccc t 31829DNAArtificial sequenceoligonucleotide
primer 8tagtataaac aatgagacac cagggatta 29938DNAArtificial
sequenceoligonucleotide primer 9ccctatttct aagtcagatc ctacatacaa
agtcatgt 381038DNAArtificial sequenceoligonucleotide primer
10ccctatttct aagtcagatc ctacatacaa agtcatgc 381127DNAArtificial
sequenceoligonucleotide primer 11cccacatcta gtactgtcac tgattga
271227DNAArtificial sequenceoligonucleotide primer 12cccacatcta
gtactgtcac tgattgt 271327DNAArtificial sequenceoligonucleotide
primer 13cccacatcta gtactgtcac tgattgc 271429DNAArtificial
sequenceoligonucleotide primer 14aagtggagaa aattagtaga tttcaggga
291527DNAArtificial sequenceoligonucleotide primer 15cccacatcta
gtactgtcac tgattgg 271627DNAArtificial sequenceoligonucleotide
primer 16ctacatacaa gtcatccata tattgcc 271727DNAArtificial
sequenceoligonucleotide primer 17ctacatacaa gtcatccata tattgct
271829DNAArtificial sequenceoligonucleotide primer 18caccagggat
tagatatcaa tataatgtg 291928DNAArtificial sequenceoligonucleotide
primer 19ctatgttgcc ctatttctaa gtcagagg 282028DNAArtificial
sequenceoligonucleotide primer 20ctatgttgcc ctatttctaa gtcagagc
282123DNAArtificial sequenceoligonucleotide primer 21aaacaatggc
cattgacaga aga 232224DNAArtificial sequenceoligonucleotide primer
22gttcataccc catccaaaga aatg 242322DNAArtificial
sequenceoligonucleotide primer 23ctccartatt tgccataaaa cg
222422DNAArtificial sequenceoligonucleotide primer 24ctccartatt
tgccataaaa ag 222522DNAArtificial sequenceoligonucleotide primer
25ctccartatt tgccataaaa ca 222622DNAArtificial
sequenceoligonucleotide primer 26ctccartatt tgccataaaa aa
222731DNAArtificial sequenceoligonucleotide primer 27ctaagtcaga
tcctacatac aagtcatccc c 312831DNAArtificial sequenceoligonucleotide
primer 28ctaagtcaga tcctacatac aagtcatccc t 312937DNAArtificial
sequenceoligonucleotide primer 29ccctatttct aagtcagatc ctacatacaa
gtcatgt 373037DNAArtificial sequenceoligonucleotide primer
30ccctatttct aagtcagatc ctacatacaa gtcatgc 373134DNAArtificial
sequenceoligonucleotide primer 31ctatttctaa gtcagatcct acatacaagt
catc 34321680DNAhuman immunodeficiency virus 32cccattagcc
ctattgagac tgtaccagta aaattaaagc caggaatgga tggcccaaaa 60gttaaacaat
ggccattgac agaagaaaaa ataaaagcat tagtagaaat ttgtacagag
120atggaaaagg aagggaaaat ttcaaaaatt gggcctgaaa atccatacaa
tactccagta 180tttgccataa agaaaaaaga cagtactaaa tggagaaaat
tagtagattt cagagaactt 240aataagagaa ctcaagactt ctgggaagtt
caattaggaa taccacatcc cgcagggtta 300aaaaagaaaa aatcagtaac
agtactggat gtgggtgatg catatttttc agttccctta 360gatgaagact
tcaggaagta tactgcattt accataccta gtataaacaa tgagacacca
420gggattagat atcagtacaa tgtgcttcca cagggatgga aaggatcacc
agcaatattc 480caaagtagca tgacaaaaat cttagagcct tttagaaaac
aaaatccaga catagttatc 540tatcaataca tggatgattt gtatgtagga
tctgacttag aaatagggca gcatagaaca 600aaaatagagg agctgagaca
acatctgttg aggtggggac ttaccacacc agacaaaaaa 660catcagaaag
aacctccatt cctttggatg ggttatgaac tccatcctga taaatggaca
720gtacagccta tagtgctgcc agaaaaagac agctggactg tcaatgacat
acagaagtta 780gtggggaaat tgaattgggc aagtcagatt tacccaggga
ttaaagtaag gcaattatgt 840aaactcctta gaggaaccaa agcactaaca
gaagtaatac cactaacaga agaagcagag 900ctagaactgg cagaaaacag
agagattcta aaagaaccag tacatggagt gtattatgac 960ccatcaaaag
acttaatagc agaaatacag aagcaggggc aaggccaatg gacatatcaa
1020atttatcaag agccatttaa aaatctgaaa acaggaaaat atgcaagaat
gaggggtgcc 1080cacactaatg atgtaaaaca attaacagag gcagtgcaaa
aaataaccac agaaagcata 1140gtaatatggg gaaagactcc taaatttaaa
ctgcccatac aaaaggaaac atgggaaaca 1200tggtggacag agtattggca
agccacctgg attcctgagt gggagtttgt taatacccct 1260cccttagtga
aattatggta ccagttagag aaagaaccca tagtaggagc agaaaccttc
1320tatgtagatg gggcagctaa cagggagact aaattaggaa aagcaggata
tgttactaat 1380agaggaagac aaaaagttgt caccctaact gacacaacaa
atcagaagac tgagttacaa 1440gcaatttatc tagctttgca ggattcggga
ttagaagtaa acatagtaac agactcacaa 1500tatgcattag gaatcattca
agcacaacca gatcaaagtg aatcagagtt agtcaatcaa 1560ataatagagc
agttaataaa aaaggaaaag gtctatctgg catgggtacc agcacacaaa
1620ggaattggag gaaatgaaca agtagataaa ttagtcagtg ctggaatcag
gaaagtacta 16803322DNAArtificial sequenceoligonucleotide primer
33ctccartatt tgccataaaa cc 223422DNAArtificial
sequenceoligonucleotide primer 34ctccartatt tgccataaaa ct
223521DNAArtificial sequenceoligonucleotide primer 35ctccartatt
tgccataaaa a 2136560PRThuman immunodeficiency virus 36Pro Ile Ser
Pro Ile Glu Thr Val Pro Val Lys Leu Lys Pro Gly Met 1 5 10 15 Asp
Gly Pro Lys Val Lys Gln Trp Pro Leu Thr Glu Glu Lys Ile Lys 20 25
30 Ala Leu Val Glu Ile Cys Thr Glu Met Glu Lys Glu Gly Lys Ile Ser
35 40 45 Lys Ile Gly Pro Glu Asn Pro Tyr Asn Thr Pro Val Phe Ala
Ile Lys 50 55 60 Lys Lys Asp Ser Thr Lys Trp Arg Lys Leu Val Asp
Phe Arg Glu Leu 65 70 75 80 Asn Lys Arg Thr Gln Asp Phe Trp Glu Val
Gln Leu Gly Ile Pro His 85 90 95 Pro Ala Gly Leu Lys Lys Lys Lys
Ser Val Thr Val Leu Asp Val Gly 100 105 110 Asp Ala Tyr Phe Ser Val
Pro Leu Asp Glu Asp Phe Arg Lys Tyr Thr 115 120 125 Ala Phe Thr Ile
Pro Ser Ile Asn Asn Glu Thr Pro Gly Ile Arg Tyr 130 135 140 Gln Tyr
Asn Val Leu Pro Gln Gly Trp Lys Gly Ser Pro Ala Ile Phe 145 150 155
160 Gln Ser Ser Met Thr Lys Ile Leu Glu Pro Phe Arg Lys Gln Asn Pro
165 170 175 Asp Ile Val Ile Tyr Gln Tyr Met Asp Asp Leu Tyr Val Gly
Ser Asp 180 185 190 Leu Glu Ile Gly Gln His Arg Thr Lys Ile Glu Glu
Leu Arg Gln His 195 200 205 Leu Leu Arg Trp Gly Leu Thr Thr Pro Asp
Lys Lys His Gln Lys Glu 210 215 220 Pro Pro Phe Leu Trp Met Gly Tyr
Glu Leu His Pro Asp Lys Trp Thr 225 230 235 240 Val Gln Pro Ile Val
Leu Pro Glu Lys Asp Ser Trp Thr Val Asn Asp 245 250 255 Ile Gln Lys
Leu Val Gly Lys Leu Asn Trp Ala Ser Gln Ile Tyr Pro 260 265 270 Gly
Ile Lys Val Arg Gln Leu Cys Lys Leu Leu Arg Gly Thr Lys Ala 275 280
285 Leu Thr Glu Val Ile Pro Leu Thr Glu Glu Ala Glu Leu Glu Leu Ala
290 295 300 Glu Asn Arg Glu Ile Leu Lys Glu Pro Val His Gly Val Tyr
Tyr Asp 305 310 315 320 Pro Ser Lys Asp Leu Ile Ala Glu Ile Gln Lys
Gln Gly Gln Gly Gln 325 330 335 Trp Thr Tyr Gln Ile Tyr Gln Glu Pro
Phe Lys Asn Leu Lys Thr Gly 340 345 350 Lys Tyr Ala Arg Met Arg Gly
Ala His Thr Asn Asp Val Lys Gln Leu 355 360 365 Thr Glu Ala Val Gln
Lys Ile Thr Thr Glu Ser Ile Val Ile Trp Gly 370 375 380 Lys Thr Pro
Lys Phe Lys Leu Pro Ile Gln Lys Glu Thr Trp Glu Thr 385 390 395 400
Trp Trp Thr Glu Tyr Trp Gln Ala Thr Trp Ile Pro Glu Trp Glu Phe 405
410 415 Val Asn Thr Pro Pro Leu Val Lys Leu Trp Tyr Gln Leu Glu Lys
Glu 420 425 430 Pro Ile Val Gly Ala Glu Thr Phe Tyr Val Asp Gly Ala
Ala Asn Arg 435 440 445 Glu Thr Lys Leu Gly Lys Ala Gly Tyr Val Thr
Asn Arg Gly Arg Gln 450 455 460 Lys Val Val Thr Leu Thr Asp Thr Thr
Asn Gln Lys Thr Glu Leu Gln 465 470 475 480 Ala Ile Tyr Leu Ala Leu
Gln Asp Ser Gly Leu Glu Val Asn Ile Val 485 490 495 Thr Asp Ser Gln
Tyr Ala Leu Gly Ile Ile Gln Ala Gln Pro Asp Gln 500 505 510 Ser Glu
Ser Glu Leu Val Asn Gln Ile Ile Glu Gln Leu Ile Lys Lys 515 520 525
Glu Lys Val Tyr Leu Ala Trp Val Pro Ala His Lys Gly Ile Gly Gly 530
535 540 Asn Glu Gln Val Asp Lys Leu Val Ser Ala Gly Ile Arg Lys Val
Leu 545 550 555 560 3721DNAArtificial sequenceoligonucleotide
primer 37tattcctaat tgaacctccc a 213821DNAArtificial
sequenceOligonucleotide primer 38tattcctaat tgaacttccc a
213922DNAArtificial sequenceOligonucleotide primer 39ctccaatatt
tgccataaaa cg 224022DNAArtificial sequenceOligonucleotide primer
40ctccagtatt tgccataaaa cg 224122DNAArtificial
sequenceoligonucleotide primer 41ctccaatatt tgccataaaa ca
224222DNAArtificial sequenceoligonucleotide primer 42ctccagtatt
tgccataaaa ca 224322DNAArtificial sequenceoligonucleotide primer
43ctccaatatt tgccataaaa cc 224422DNAartificial
sequenceoligonucleotide primer 44ctccaatatt tgccataaaa ct
224522DNAartificial sequenceoligonucleotide primer 45ctccagtatt
tgccataaaa cc 224622DNAartificial sequenceoligonucleotide primer
46ctccagtatt tgccataaaa ct 224722DNAArtificial
sequenceoligonucleotide primer 47ctccaatatt tgccataaaa aa
224822DNAArtificial Sequenceoligonucleotide primer 48ctccaatatt
tgctataaag aa 22
* * * * *
References